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Exhibit 99.6

CERTIFICATION

I, Gilmour Clausen, certify that:

1 I have reviewed this annual report on Form 40-F of Augusta
Resource Corporation;

2. Based on my knowledge, this report does not contain any
untrue statement of a material fact or omit to state a material fact necessary
to make the statements made, in light of the circumstances under which such
statements were made, not misleading with respect to the period covered by this
report;

3. Based on my knowledge, the financial statements, and other
financial information included in this report, fairly present in all material
respects the financial condition, results of operations and cash flows of the
issuer as of, and for, the periods presented in this report;

4. The issuers other certifying officer(s) and I are
responsible for establishing and maintaining disclosure controls and procedures
(as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal controls
over financial reporting (as defined in Exchange Act Rules 13a-15(f) and
15d-5(f) for the issuer and have:

(a) Designed such disclosure
controls and procedures, or caused such disclosure controls and procedures to be
designed under our supervision, to ensure that material information relating to
the issuer, including its consolidated subsidiaries, is made known to us by
others within those entities, particularly during the period in which this
report is being prepared;

(b) Designed such internal
control over financial reporting, or caused such internal control over financial
reporting to be designed under our supervision, to provide reasonable assurance
regarding the reliability of financial reporting and the preparation of
financial statements for external purposes in accordance with generally accepted
accounting principles;

(c) Evaluated the effectiveness of the
issuers disclosure controls and procedures and presented in this report our
conclusions about the effectiveness of the disclosure controls and procedures,
as of the end of the period covered by this report based on such evaluation; and

(d) Disclosed in this report any
change in the issuers internal control over financial reporting that occurred
during the period covered by the annual report that has materially affected, or
is reasonably likely to materially affect, the issuers internal control over
financial reporting; and

5. The issuers other certifying officer(s) and I have
disclosed, based on our most recent evaluation of internal control over
financial reporting, to the issuers auditors and the audit committee of the
issuers board of directors (or persons performing the equivalent functions):

(a) All significant deficiencies and
material weaknesses in the design or operation of internal control over
financial reporting which are reasonably likely to adversely affect the issuers
ability to record, process, summarize and report financial information; and

(b) Any fraud, whether or not
material, that involves management or other employees who have a significant
role in the issuers internal control over financial reporting.

|Date: March 31, 2014 | By: | /s/
      Gilmour Clausen                   
|-------------------- | --- | --------------------------------------------
|                     |     |                                             
|                     |     | Name: Gilmour Clausen                       
|                     |     | Title: President and Chief Executive Officer

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