Fuel Fraud Prevention Act of 2003 - Amends the Internal Revenue Code concerning collecting taxes on and providing for the accountability of fuel, including: (1) providing for the taxation of aviation fuel upon its removal from any refinery or terminal, entry into the United States, and upon its sale; (2) establishing penalties for tampering with a mechanical dye injection system used to indelibly dye fuel and operators of such systems failing to maintain security standards to be established; (3) making fuel tax records available to Federal Department of Transportation; (4) granting the Secretary of the Treasury authority to inspect any books and records and shipping papers pertaining to fuel at any production or storage site; (5) expanding registration and reporting requirements with respect to those handling fuel; (6) taxing unregistered importers at point of entry; and (7) dedicating certain penalties to the Highway Trust Fund.