To extend certain immigration programs, and for other purposes.

Employee Verification Amendment Act of 2009 - Amends the Illegal Immigration Reform and Immigrant Responsibility Act of 1996 to extend the employment eligibility confirmation pilot programs (which includes the E-Verify basic pilot program) until September 30, 2014.

Directs the Commissioner of Social Security and the Secretary of Homeland Security to enter into a fiscal year agreement which shall: (1) provide funds to the Commissioner for such programs' full costs in quarterly advances; and (2) require an annual accounting and reconciliation of costs incurred and funds provided. Provides for funding continuation in the absence of an agreement.

Requires that the Government Accountability Office (GAO) conduct studies regarding: (1) erroneous tentative nonconfirmations under the E-Verify program; and (2) such program's effects on small entities.

Amends the Departments of Commerce, Justice, and State, the Judiciary, and Related Agencies Appropriations Act, 1993 to extend the alien investor (EB-5) regional center program through FY2014.

Amends the Immigration and Nationality Act to extend the special immigrant program for non-minister religious workers until September 30, 2014.

Amends the Immigration and Nationality Technical Corrections Act of 1994 to extend the J-1 visa waiver (Conrad state 30/medical services in underserved areas) program until September 30, 2014.