<PAGE>

                                                                   Exhibit 10.16


                       CONTRACT MANUFACTURING AGREEMENT

     This Contract Manufacturing Agreement (this "Agreement") is entered into as
of March 31, 2001, between Millipore Corporation ("Millipore"), a Massachusetts
corporation with its principal place of business at 80 Ashby Road, Bedford, MA
01730, and Mykrolis Corporation ("Mykrolis"), a Delaware corporation with its
principal place of business at Patriots Park, Bedford, MA 01730.

                                   RECITALS

     1.   Millipore currently owns all of the issued and outstanding common
stock of Mykrolis.

     2.   Millipore and Mykrolis have entered into a Master Separation and
Distribution Agreement as of March 28, 2001 (the "Master Agreement") under
which, among other things, the business of Millipore's Microelectronics Division
is to be taken over by, and the assets and liabilities associated therewith are
to be transferred to and assumed by, Mykrolis at the Separation Date (as defined
in the Master Agreement).

     3.   After the Separation Date, in order to enable Mykrolis to carry on its
respective business as a separate company, Mykrolis wishes that Millipore, on a
contract manufacturing basis, supply the product (or products) listed on Exhibit
A (the "Product") to Mykrolis, and Millipore wishes to do so.

     4.   The Master Agreement provides for this Agreement to be entered into as
of the Separation Date.

     NOW, THEREFORE, in consideration of the foregoing and the covenants and
agreements set forth below, the parties hereto agree as follows:

1.   Definitions.  Capitalized terms defined in this Agreement shall have the
     -----------
respective meanings assigned to them at the location of their definition.
Capitalized Terms used in this Agreement without definition which are defined in
the Master Agreement shall have the meaning ascribed thereto in the Master
Agreement.

2.   Overriding Character of this Agreement
     --------------------------------------

     A.   Unless otherwise agreed by both parties in writing, this Agreement
          applies to all purchase releases, purchase orders and other documents
          of purchase for the Products (hereinafter collectively referred to as
          "Releases") which Mykrolis may place with Millipore during the term of
          this Agreement.  The terms and conditions of this Agreement shall
          apply to any Releases, whether or not this Agreement or its terms and
          conditions are expressly referenced in the Release.
<PAGE>

     B.   Unless otherwise agreed by both parties in writing for a specific
          transaction, no inconsistent or additional term or condition in any
          Release shall be applicable to a transaction within the scope of this
          Agreement.  Both parties specifically agree that any term and
          condition on any of their purchase or sale documents used as Releases
          hereunder which are in any way inconsistent with this Agreement shall
          be inapplicable, and the terms of this Agreement shall govern.

3.   Supply of Product
     -----------------

     (a)  Millipore agrees to sell to Mykrolis, from time to time during the
          Term, Product, in the amounts contained in Mykrolis's Releases.
          Except as set forth in Section 6(a) hereof, Mykrolis shall have no
          minimum or maximum purchase requirements for the Products.

     (b)  Millipore agrees to manufacture and package the Products in accordance
          with the specifications therefor in effect as of the Separation Date.
          In addition, Millipore agrees to label and otherwise mark the Products
          and the packaging for the Products with Mykrolis's trademarks and
          trade names in accordance with artwork specified by Mykrolis.  Except
          as otherwise expressly agreed, Mykrolis agrees that it shall not
          resell the Products under  any Millipore trademark or trade name.

4.   Term and Termination
     --------------------

     (a)  The effective period of this Agreement (the "Term") shall begin on the
          Separation Date and continue thereafter for a period of five (5) years
          or until earlier termination in accordance with clause (b) or (c) of
          this Section 4. Any Release issued by Mykrolis before the effective
          date of termination and in accordance with Section 6(a) hereof shall
          be fulfilled by Millipore.

     (b)  Either party may terminate this Agreement prior to the expiration of
          the Term without prejudice to any rights or liabilities accruing up to
          the date of termination:

          (i)  in the event of a material breach by the other party of any of
               the terms and conditions of this Agreement, by giving the other
               party notice of such breach, and provided that such breach shall
               not have been cured, or material steps to effect a cure
               undertaken within sixty (60) days following such notice; and

          (ii) immediately, by written notice thereof, if any of the following
               events or an event analogous thereto occurs:

               a.   an adjudication has been made that the other party is
                    bankrupt or insolvent;

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               b.   the other party has filed bankruptcy proceedings or has had
                    such proceedings filed against it, except as part of a bona
                    fide scheme for reorganization;

               c.   a receiver has been appointed for all or substantially all
                    of the property of the other party;

               d.   the other party has assigned or attempted to assign this
                    Agreement for the benefit of its creditors; or

               e.   the other party has begun any proceeding for the liquidation
                    or winding up of its business affairs.

     (c)  Mykrolis may terminate this Agreement effective at any time, provided
          it has given Millipore at least sixty (60) days prior written notice
          thereof.

     (d)  Termination under this Section 4 shall be in addition to and not a
          substitute for other rights or causes of action of the terminating
          party.

5.   Price
     -----

     (a)  For the first year of this Agreement, the price shall be as set forth
          on Exhibit A, which is attached and incorporated by reference.
          Thereafter, Millipore shall be entitled to adjust prices annually on
          each anniversary of the Separation Date in order to recoup actual
          increases in the cost to manufacture the Products.  Millipore agrees
          to justify any price increases hereunder by an open-book review of its
          costs with Mykrolis.

     (b)  Prices and deliveries will be FOB the Millipore plant which is
          producing the Product.

6.   Orders, Delivery and Payment
     ----------------------------

     (a)  Mykrolis will provide Millipore with a rolling one year forecast of
          its demand for Product hereunder (a "One-Year Forecast") which will be
          updated on a quarterly basis, at least thirty (30) days prior to the
          start of each calendar quarter. Each such One-Year Forecast shall
          include a sub-forecast for the first three months within the One-Year
          Forecast (a "3 Month Forecast"). Mykrolis shall provide Releases for
          delivery, during the three months covered by such 3 Month Forecast, in
          the quantities specified therein, but subject to increase or reduction
          in such quantities of not more than 25%. Except for such purchase
          commitment in the 3 Month Forecasts, the One-Year Forecasts will be
          used for planning purposes only and are not binding. Millipore will
          ship Product so as to arrive on the delivery date set forth in a
          Release, provided that the delivery date

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<PAGE>

          set forth in such Release is not less than 30 days following the date
          Millipore receives such Release and provided that the amounts set
          forth in such Release are within the range provided above in
          accordance with the applicable 3 Month Forecast.

     (b)  Mykrolis shall make payment to Millipore within forty-five (45) days
          after the later of (i) receipt of the Product, and (ii) receipt of
          Millipore's invoice for the Product. All payments shall be made in
          U.S. Dollars. Late payments shall bear interest at a rate of 12% per
          annum.

     (c)  All Product shall be tested, inspected and packaged for delivery by
          Millipore as mutually agreed by the parties.

     (d)  Millipore shall make reasonable best efforts to ship the Product in
          accordance with the requested delivery dates.  Millipore shall give
          prompt notice of any delay in shipment and shall use diligence to
          remove the cause of any such delay, provided, however, that Millipore
                                              --------  -------
          accepts no liability for general, special, or consequential damages
          arising out of delay in delivery.

     (e)  Identification of the Products to this Agreement shall occur when they
          are packed for shipment, addressed to Mykrolis and delivered to a
          common carrier, at which time title and risk of loss shall pass to
          Mykrolis.  In the event that any shipment of Products or any portion
          thereof fails to conform to the applicable specifications, then
          Mykrolis shall be entitled to reject such shipment of Products or the
          portion thereof that fails to so conform, as the case may be.
          Mykrolis shall communicate its rejection hereunder by written notice,
          given within twenty (20) days following the date on which such
          shipment was received by Mykrolis, specifying the grounds for such
          rejection.  If no written notice of rejection is given by Mykrolis
          within said twenty (20) day period, the Products shall be deemed to
          have been accepted, and to have conformed to the applicable
          specifications.  In the event of any proper and timely rejection,
          Millipore agrees:  (i) that it shall bear the cost of shipment for the
          return of rejected Products and (ii) to use its reasonable best
          efforts to cure such rejection or replace such nonconforming Products
          within thirty (30) days after receipt of written notice thereof.

7.   Special Covenants.
     ------------------

     (a)  Millipore agrees that the Products are exclusively Mykrolis Products
          and that Millipore agrees that neither it nor any of its Subsidiaries
          shall manufacture, market or sell the Products to any person other
          than Mykrolis or its Subsidiaries.  Notwithstanding the above, if any
          Product is covered by the Product Distribution Agreement entered into
          by Millipore and Mykrolis

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<PAGE>

          pursuant to the Master Agreement, then Millipore may distribute that
          Product as per the terms of such Product Distribution Agreement.

     (b)  Mykrolis agrees that neither it nor any of its subsidiaries will (i)
          sell the Product into the Millipore Core Business, or (ii) grant any
          distributor, OEM manufacturer or other third party the right or permit
          any of them to sell the Products into the Millipore Core Business

8.   Warranties
     ----------

     Millipore Corporation ("Millipore") warrants the Products will be free
     from defects in materials and workmanship when used in accordance with the
     applicable instructions for a period of one year from shipment of the
     Products.  MILLIPORE MAKES NO OTHER WARRANTY, EXPRESSED OR IMPLIED.  THERE
     IS NO WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The
     warranty provided herein and the data, specifications and descriptions of
     Millipore products appearing in Millipore's published catalogues and
     product literature may not be altered except by express written agreement
     signed by an officer of Millipore.  Representations, oral or written, which
     are inconsistent with this warranty or such publications are not authorized
     and if given, should not be relied upon.

     In the event of a breach of the foregoing warranty, Millipore's sole
     obligation shall be to repair or replace, at its option, the applicable
     Product or part thereof, provided Mykrolis notifies Millipore promptly of
     any such breach.  If after exercising reasonable efforts, Millipore is
     unable to repair or replace the Product or part, then Millipore shall
     refund to Mykrolis all monies paid for such applicable product or part.
     MILLIPORE SHALL NOT BE LIABLE FOR CONSEQUENTIAL, INCIDENTAL, SPECIAL OR ANY
     OTHER INDIRECT DAMAGES RESULTING FROM ECONOMIC LOSS OR PROPERTY DAMAGE
     SUSTAINED BY ANY CUSTOMER FROM THE USE OF ITS PRODUCTS.

9.   Product Modifications
     ---------------------

     Millipore agrees that it will not materially change the Product that it
     will supply hereunder or their formulation, manufacturing or testing
     processes, process equipment, other aspects of form, fit or function, or
     production location, unless Mykrolis approves such change in writing, which
     approval may require formal validation and qualification and possibly
     customer notification.  The implementation of any such accepted changes
     shall be subject to the parties' agreement on any change in price or other
     terms of supply as may be necessitated or requested by a party as a result
     of such change.

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<PAGE>

10.  Inventory
     ---------

     Millipore will maintain an inventory of Product, in such amounts as shall
     be agreed by the parties but in no event less than amounts specified in
     Mykrolis's current 3 Month Forecast.

11.  Access to Facilities
     --------------------

     At any time during the Term, upon reasonable advance notice by Mykrolis,
     Mykrolis's authorized representatives and customers (subject to appropriate
     confidentiality obligations) shall be provided access to the facilities of
     Millipore to audit or verify conformity of Product manufacture to
     specifications.

12.  Notices
     -------

     Any notice or other communication required or permitted to be given by
     either party pursuant to the terms of this Agreement shall be in writing
     and shall be deemed given if and when delivered by hand or sent by
     certified mail, return receipt requested, overnight courier, confirmed
     telecopy, or confirmed electronic mail transmission, addressed as follows:

          If to Millipore:         Millipore Corporation
                                   80 Ashby Road
                                   Bedford, MA  01730
                                   Attn:Vice President, Manufacturing
                                        -----------------------------
                                   Fax: [(781)__________]


          with a copy to:          Millipore Corporation
                                   80 Ashby Road
                                   Bedford, MA 01730
                                   Attn:  General Counsel
                                   Fax:  (781) 533-3125


          If to Mykrolis:          Mykrolis Corporation
                                   Patriots Park
                                   Bedford, MA  01730
                                   Attn:Vice President, Manufacturing
                                        -----------------------------
                                   Fax:  [(781) ________]


          with a copy to:          Mykrolis Corporation
                                   Patriots Park
                                   Bedford, MA  01730

                                       6
<PAGE>

                                   Attn:  General Counsel
                                   Fax:  (781) _________


     or to such electronic mail address as may be specified by an addressee
     party to the other party by one of the other means provided above, or to
     such other address, telecopy number or electronic mail address as may be
     specified by an addressee party to the other by one of the means provided
     above.

13.  Force Majeure
     -------------

     The obligations of a party under this Agreement will be suspended to the
     extent that it is wholly or partially precluded from complying with its
     obligations under this Agreement by force majeure.  Force majeure includes,
     but is not restricted to, fire, storm, flood, earthquake, explosion,
     accident, act of the public enemy, war, rebellion, insurrection, sabotage,
     epidemic, quarantine restriction, labor dispute, labor shortage,
     transportation embargo or failure or delay in transportation, act of God,
     act (including laws, regulations, disapprovals or failure to approve) of
     any government agency, whether national, municipal, or otherwise. The
     parties shall be relieved of their respective obligations hereunder, to the
     extent that the performance of such obligation was actually prevented
     thereby.  During the existence of any such condition, the affected party
     shall, nevertheless, use its best efforts to remove the cause thereof.

14.  No Other Rights
     ---------------

     Neither party shall have any rights hereunder to any patents or other
     intellectual property of the other party, except as specifically set forth
     herein.

15.  Incorporation of Provisions from Master Agreement
     -------------------------------------------------

     The following provisions of the Master Agreement, mutatis mutandis, are
                                                       ------- --------
     hereby incorporated by reference into this Agreement for all purposes:

          Article VI (Confidentiality);
          Article IX (Dispute Resolution);
          Section 10.3 (Governing Law);
          Section 10.6 (Counterparts);
          Section 10.7 (Binding Effect; Assignment);
          Section 10.8 (Severability);
          Section 10.9 (Failure or Indulgence Not Waiver;
                           Remedies Cumulative);
          Section 10.10 (Amendment);
          Section 10.11 (Authority);
          Section 10.12 (Interpretation).

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<PAGE>

     In the event of any conflict between any of the foregoing incorporated
     provisions of the Master Agreement and any other provision of this
     Agreement, such other provisions shall prevail.

16.  Entire Agreement
     ----------------

     This Agreement, including Exhibit A attached hereto, is the entire
                               ------- -
     agreement between the parties with respect to the subject matter hereof,
     and supersedes any prior negotiations and agreements or understandings and
     any contemporaneous oral agreements or understandings with respect to the
     subject matter hereof.

     IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be
executed by their duly authorized representatives effective as of the date first
set forth above.

MILLIPORE CORPORATION              MYKROLIS CORPORATION


By: /s/ Francis J. Lunger          By: /s/ Jean-Marc Pandraud
   -----------------------------       ------------------------
Name: Francis J. Lunger            Name: Jean-Marc Pandraud
      --------------------------         ----------------------
Title: Executive Vice President    Title: President
       -------------------------          ---------------------

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<PAGE>

                        EXHIBIT A:  Product and Prices



Products:      .  Fluorogard cartridges with sales during the previous two years
                  before the effective date of this Agreement.

                  From Bedford Molding:
                  --------------------

                  . 16908       Slipper
                  . 40640       ILM
                  . 41641       ILM
                  . 42172       HF Top Cap
                  . 42173       HF Bottom Cap
                  . 43014       LHVD Hsg Bowl
                  . 43015       LHVD Hsg Head
                  . 95977       CMP End Cap
                  . 95978       CMP End Cap
                  . 95979       CMP End Cap
                  . 108318      CMP Slipper
                  . 108184      LHVD Potting Disk
                  . 108488      Solaris C-ring
                  . 108489      Solaris Solid Ring
                  . 108995      Filter Guide
                  . 108996      Filter Guide
                  . 108997      Pivot
                  . 108998      Latch Slide
                  . 108999      Release Tab

                  From Jaffrey Molding:
                  --------------------

                  . 12596X2     Halar disk
                  . 15051       1/4" VCR protective cap
                  . 15050       3/8" VCR protective cap
                  . 12597       Endcap
                  . 12598       Endcap
                  . 15122X1     WWFG 1" Dustcap (red)
                  . 15122X2     WWFG 1" Dustcap (clear)
                  . 16946X      PFA cap CD 0
                  . 15121X2     Mini-WWFG dustcap
                  . 12747       Endcap
                  . 13290       Adapter Dbl o-ring
                  . 95894       Housing inlet cap
                  . 95895       Housing outlet cap
                  . 16040       Hsg outlet 1/4 NPTF
                  . 16041       Hsg outlet 1/2 NPTM
                  . 16042       Hsg inlet 1/4 NPTF
                  . 16043       Hsg inlet 1/2 NPTM
                  . 15411X2     Dust cap  clear WWFG
                  . 12797       Caplug NPT Wafergard

                                       9
<PAGE>

                  . 15315       Int o-ring adapt Halar
                  . 43014       LHVD IntelliGen Hsg bowl
                  . 43015       LHVD IntelliGen Hsg head
                  . 108491      Solaris end cap


                  Other BioP Assemblies Used In MiE Products:
                  -------------------------------------------

                  . 108898X3    Pegasus Subassy
                  . 108898X7    Pegasus Subassy
                  . 108898X8    Pegasus Subassy
                  . 12676       Slit Patapar
                  . 95049       Chempure Pleated Cart
                  . 12418       Cartridge Wafer-6 w/2-012
                  . Molsheim    Engineering Filter Housing's
                    Engineered  assembly equipment for
                    Systems     microelectronics applications*
                    Plant


Initial Price
for All Products:   Millipore Standard Cost as of the effective date of this
                    Agreement as set forth in Millipore's Oracle System, plus
                    ten percent of such standard cost.



* Because this Product is not an exclusively Mykrolis product, Section 7(A) of
this Agreement does not apply with respect to this Product.

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