War Funding Accountability Act of 2003 - Authorizes emergency supplemental appropriations for the reconstruction of Iraq and Afghanistan and the war on terrorism for FY 2004 to be made available only in allotments of $20 billion or less and only if the President submits a report to Congress that: (1) describes the purpose of each program to receive $1 million or more; (2) describes the purpose and contract for any allotment for rehabilitation or reconstruction; (3) describes progress being made to restore self-government, provide civil services, and ensure adequate security for the Iraqi people; (4) surveys the security, infrastructure, and other needs in Iraq and Afghanistan; (5) assesses other security and reconstruction needs in Iraq and Afghanistan; (6) describes efforts to obtain increased assistance from other countries; and (7) describes efforts to provide adequate deployment rotation and other relief for U.S. troops in Iraq.