Exhibit 99.(3)(46) AMENDMENT TO THE INVESTMENT ADVISORY AGREEMENT (HARBOR SHORT DURATION FUND) This Amendment ("Amendment") is made as of March 1, 2007 to the Investment Advisory Agreement, dated March 1, 2002, between Harbor Capital Advisors, Inc....

                                                              Exhibit 99.(3)(46)

                 AMENDMENT TO THE INVESTMENT ADVISORY AGREEMENT
                          (HARBOR SHORT DURATION FUND)

This Amendment ("Amendment") is made as of March 1, 2007 to the Investment
Advisory Agreement, dated March 1, 2002, between Harbor Capital Advisors, Inc.
(the "Adviser") and Harbor Funds (the "Trust"), on behalf of Harbor Short
Duration Fund (the "Agreement").

     WHEREAS, the parties agree to amend Paragraph 6, Compensation of the
Adviser, of the Agreement to reduce the rate at which the Trust compensates the
Adviser with respect to the Harbor Short Duration Fund;

     NOW, THEREFORE, the parties agree as follows:

     1    Paragraph 6, Compensation of the Adviser, Line 3, the following is
          deleted:

               ".30% per annum of the average daily net assets"

          and the following is inserted in its place:

               ".20% per annum of the average daily net assets".

     2    Except as specifically set forth herein, all other provisions of the
          Agreement shall remain in full force and effect.

IN WITNESS WHEREOF, the parties have executed this Amendment as of the date set
forth above.

HARBOR FUNDS ON BEHALF OF
HARBOR SHORT DURATION FUND               HARBOR CAPITAL ADVISORS, INC.

By: /s/ Xxxxx X. Xxx Xxxxxx              By: /s/ Xxxxxxx X. XxXxxx
    ----------------------------             --------------------------------

Name: Xxxxx X. Xxx Xxxxxx                Name:Xxxxxxx X. XxXxxx

Title: President                         Title: Executive Vice President