Exhibit 10.4

THIS FIRST AMENDMENT TO THE REGISTRATION RIGHTS AGREEMENTS (this “Amendment”) is
made as of April 3, 2012, by and among Horizon Lines, LLC, a Delaware limited
liability company (the “Company”), Horizon Lines, Inc. and its subsidiaries set
forth on the signature page hereto (collectively, the “Guarantors”) and the
Purchasers, governing each of the Company’s (i) 11.0% Senior Secured Notes due
2016 and (ii) Second Lien Senior Secured Notes due 2016. The Company, the
Guarantors and the Purchasers are sometimes referred to herein individually as a
“Party” and collectively as the “Parties”. Capitalized terms used herein but not
defined herein shall have the meanings given to such terms in the Registration
Rights Agreements (as herein defined).

WHEREAS:

(A) The Parties entered into that certain Registration Rights Agreement in
relation to the First-Lien Notes (the “First-Lien Registration Rights
Agreement”) dated as of October 5, 2011.

(B) The Parties entered into that certain Registration Rights Agreement in
relation to the Second-Lien Notes (the “Second-Lien Registration Rights
Agreement” and, together with the First-Lien Registration Rights Agreement, the
“Registration Rights Agreements”) dated as of October 5, 2011.

(C) The Parties hereto desire to amend each of the Registration Rights
Agreements as set forth in this Amendment.

NOW, THEREFORE, in consideration of the premises and the agreements, provisions
and covenants herein contained, the Parties hereby agree as follows:

1. The second sentence of the first paragraph of Section 3.1(a) of each of the
Registration Rights Agreements is hereby deleted in its entirety and replaced
with the following:

“Each of the Company and the Guarantors shall use commercially reasonable
efforts to Consummate the Exchange Offer as soon as practicable after the
Closing Date, but in any event not later than 300 days following the Closing
Date (such 300th day being the “Exchange Date”).”

2. This Amendment amends solely the provisions of the Registration Rights
Agreements set forth herein and nothing in this Amendment is intended or shall
be construed as amending or waiving any other terms or provisions of the
Registration Rights Agreements or any other rights of the Parties under the
Registration Rights Agreements. The Parties acknowledge that the Registration
Rights Agreements (as amended by this Amendment) are in full force and effect
and is hereby confirmed and ratified in all respects. References in each of the
Registration Rights Agreements to the relevant Registration Rights Agreement
shall mean the relevant Registration Rights Agreement as amended by this
Amendment.

3. This Amendment may be executed in any number of counterparts (including by
facsimile), each of which will be an original with the same effect as if the
signatures thereto and hereto were upon the same instrument. This Amendment
shall become effective when each Party shall have received counterparts hereof
signed by all of the other Parties.

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4. Each Purchaser that executes this Amendment hereby represents, with respect
to itself only, that it holds the securities set forth on its signature page as
of the date hereof.

5. THIS AMENDMENT SHALL BE GOVERNED BY AND CONSTRUED IN ACCORDANCE WITH THE LAWS
OF THE STATE OF NEW YORK, WITHOUT REGARD TO THE CONFLICTS OF LAW RULES THEREOF.

[signature pages follow]

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IN WITNESS WHEREOF, the parties have executed this First Amendment to the
Registration Rights Agreements as of the date first written above.

 

HORIZON LINES, LLC. By:  

 

  Name:   Michael F. Zendan II   Title:   Secretary HORIZON LINES, INC. HORIZON
LINES HOLDING CORP. HAWAII STEVEDORES, INC. HORIZON LINES OF PUERTO RICO, INC.
HORIZON LINES OF ALASKA, LLC HORIZON LINES OF GUAM, LLC HORIZON LINES VESSELS,
LLC H-L DISTRIBUTION SERVICE, LLC HORIZON LOGISTICS, LLC AERO LOGISTICS, LLC
SEA-LOGIX, LLC HORIZON SERVICES GROUP, LLC By:  

 

  Name:   Michael F. Zendan II   Title:   Secretary

[Signature Page to First Amendment to Registration Rights Agreements]

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The foregoing First Amendment to the Registration Rights Agreements is hereby
confirmed and accepted as of the date first above written:

 

By:   [                    ] By:  

 

  Authorized Signatory:

$[            ] in aggregate principal amount of 11.00% First Lien Senior
Secured Notes due 2016 issued by Horizon Lines, LLC

$[            ] in aggregate principal amount of Second Lien Senior Secured
Notes due 2016 issued by Horizon Lines, LLC.

[Signature Page to First Amendment to Registration Rights Agreements]