Interstate Tolls Relief Act of 1999

Interstate Tolls Relief Act of 1999 - Amends the Transportation Equity Act for the 21st Century to repeal the Interstate System Reconstruction and Rehabilitation pilot program.

Amends Federal transportation law to direct the Secretary of Transportation to permit Federal participation in reconstruction or replacement of a toll-free tunnel.

Specifies that before the Secretary may permit Federal participation in construction of a highway, bridge, or tunnel located in a State, the public authority having jurisdiction must enter into an agreement with the Secretary which provides that all toll revenues received from the operation of the toll facility will be used only for debt service, reasonable return on investment of any private person financing the project, and the costs necessary for the proper operation and maintenance of the toll facility.

Repeals a provision allowing the State, upon certifying annually that the tolled facility is being adequately maintained, to use any toll revenues in excess of amounts so required for any purpose for which Federal funds may be obligated by a State under Federal transportation provisions.