Department of Homeland Security Financial Accountability Act

Department of Homeland Security Financial Accountability Act - (Sec. 3) Amends the Chief Financial Officer Act of 1990 and the Homeland Security Act of 2002 to require the President to appoint, subject to Senate confirmation, a Chief Financial Officer (CFO) for the Department of Homeland Security (DHS), who is to report directly to the Secretary of DHS and to the Under Secretary for Management.

Requires the President to appoint or designate a CFO of DHS within 180 days after enactment of this Act. Permits the current CFO to continue to serve until confirmation or designation of a successor.

Removes the Federal Emergency Management Agency (FEMA) from the list of agencies required to have a CFO.

(Sec. 4) Amends the Reports Consolidation Act of 2000 to instruct the Secretary of DHS to: (1) submit for each fiscal year a performance and accountability report that incorporates a certain program performance report for the DHS; (2) include in each such report for fiscal years after FY 2004 an audit opinion of DHS internal controls over its financial reporting; and (3) design and implement DHS-wide management controls that reflect the national homeland security strategy of the Homeland Security Act of 2002, and that permit assessment by Congress and DHS managers of DHS performance in executing such strategy.

Requires performance and accountability reports for FY 2004 to include an assertion of the internal controls that apply to financial reporting by the DHS.

Directs the Chief Financial Officers Council and the President's Council on Integrity and Efficiency to conduct a joint study, and report to specified congressional committees and to the Comptroller General, on the potential costs and benefits of requiring certain CFO agencies to obtain audit opinions of their internal controls over their financial reporting.

Instructs the Comptroller to analyze such results and report on them to the same congressional committees.

(Sec. 5) Directs the Secretary of DHS to develop, and update annually, a comprehensive national homeland security strategy containing specified elements.

(Sec. 6) Amends the Homeland Security Act of 2002 to instruct the Secretary to establish an Office of Program Analysis and Evaluation to analyze and evaluate plans, programs, and budgets of DHS in relation to homeland security objectives, projected threats, vulnerability assessments, estimated costs, resource constraints, and the national homeland security strategy.

Creates the position of Director of Program Analysis and Evaluation as principal staff assistant to the CFO of the DHS for program analysis and evaluation.

(Sec. 7) Requires the CFO of DHS to notify simultaneously specified congressional committees whenever appropriations that are available to either DHS or any DHS officer are transferred or reprogrammed and notice of such transfer or reprogramming is submitted to Congress.

(Sec. 8) Authorizes appropriations.