Migratory Bird Treaty Reform Act of 2004

Title I: Exclusion of Nonnative Species from Migratory Bird Treaty Act - Migratory Bird Treaty Reform Act of 2004 - (Sec. 102) Amends the Migratory Bird Treaty Act (MBTA) to clarify that the MBTA's prohibition on taking, killing, or possessing migratory birds applies only to native migratory bird species whose occurrence in the United States results from natural biological or ecological conditions.

Excludes from coverage under the MBTA bird species occurring as the result of human assisted introduction unless the species: (1) was native to the United States and extant in 1918; (2) became extinct throughout its range thereafter; and (3) was reintroduced as part of a Federal program.

(Sec. 103) Requires the Secretary of the Interior (the Secretary) to publish a list of all non-native, human introduced bird species to which the MBTA does not apply that belong to biological families of migratory birds covered under any migratory bird conventions with Great Britain (for Canada), Mexico, Russia, or Japan.

Title II: Conservation of Neotropical Migratory Birds - Neotropical Migratory Bird Conservation Improvement Act of 2004 - (Sec. 202) Amends the Neotropical Migratory Bird Conservation Act (NMBCA) to increase the Federal share of costs for projects funded under that Act. Prescribes the form of payment for such projects undertaken in the United States and Canada versus Latin America and the Caribbean.

Establishes the Neotropical Migratory Bird Conservation Fund.

Increases the amount of funds that the Secretary may expend to administer the NMBCA.

Authorizes the Secretary of the Treasury to transfer to the Fund amounts that were in the Neotropical Migratory Bird Conservation Account immediately before the enactment of this Act.

Authorizes appropriations. Requires not less than 75 percent of such appropriations to be used for projects outside the United States. Prohibits expenditures for projects in Canada during a fiscal year unless the amount available to carry out NMBCA exceeds $10 million for that year.