The American Public Tranist Association, trade group for most of the nation's 1,034 urban transportation system, filed suit yesterday to block new federal regulations that would require all subways and buses to be fully accessible to handicapped passengers.

In a complaint filed in U.S. District Court, the association said the new rules, scheduled to go into effect Monday, would more than $5 billion in new equipment and facilities without any assurance of increased federal subsidies.

The figure is about three times the $1.8 billion cost estimate made by the Department of Transportation, which issued the new rules with concurrence from the Department of Health, Education and Welfare.

The suit seeks an injunction to prohibit the Transportation Department from enforcing the rules.

Its filing brings into sharp focus a growing dispute between the transit industry and organizations of handicapped people, who conten they are deprived of publicly financed facilities available to all others.

In public hearings after the rules were proposed last year, spokesmen said full accessibility boils down to a civil rights issue.

Under the rules, one-third of existing stations on older sybway systems in such cities as New York and Chicago must be made accessible.

New rail systems, such as Washington's Metro, have been constructed with elevators for the handicapped in addition to escalators or stairways for other riders. The elevators were added in Washington after a local coalition of handicapped groups won a lawsuit requiring their installation.

The rules also require that, within 10 years, half of all transit buses used with lifts to permit wheelchair users to get on and off.

All transit buses built in this country since 1977 have been manufactured so they could be equipped with lifts. In Washington Metro's latest bus order, 130 buses were equipped with lifts. New schedules that go into effect here tomorrow list specific trips on many routes on which those lift-equipped buses will be operated.

The new rules also require that commuter railway stations and trolley terminals be fully accessible, and that all new rail equipment have special provisions for wheelchair users.

The 94 new rail cars that Metro formally ordered this week will have some retractable seats to provide special space for wheelchairs.

In its lawsuit, the transit association contended that the existing rules, adopted in 1976, are adequated. They generally permit communities to decide for themselves how to meet the transportation needs of the elderly and handicapped, without spelling it out.

The association cited as a precedent a June 11 decision by the Supreme Court, which held that a college did not have to provide special facilities for a handicapped applicant for enrollment - a deaf woman - simply because the college received federal funds. Most transit systems are federally subsidized.

The suit was filed in the name of the association, which has its headquarters in Washington, along with 12 transit systems around the country that are among its members. Washington's Metro, a member, is not of the plaintiffs.