The House Public Works Committee yesterday raised the first official congressional challenge to regulations that require subways and buses be accessible to wheelchairs.

The challenge came in a bill that authorizes $27.7 billion in federal aid for the next five years to public transit systems.As sent to the full House, the bill would permit local transit systems to set up special service for handicapped persons instead of requiring them to buy all-accessible new vehicles or refit old equipment, as they must now do under federal Department of Transportation regulations.

Representatives of several handicapped organizations said yesterday that they fear the committee action was just the first in many that will chip away at what they regard as hard-won civil rights.

The transportation regulations are among the most expensive to implement of all the handicapped rules, which have resulted in wider doors in public buildings, the elimination of curbs and the placement of elevators in low-rise schools.

Department of Transportation regulations require that all new buses and subway cars must be accessible to wheelchair users, as must all commuter rail cars bought after Jan. 1, 1983. Existing subway systems -- such as those in Boston and New York -- also must be made accessible over a period of years, although some waivers are possible.

DOT claimed that those changes would cost $6 billion to $8 billion. The American Public Transit Association (APTA), which represents most public transit systems in the country, claimed the minimum price would be about $20 billion.

APTA also said that fully accessible transit facilities would serve only a small portion of the handicapped people who needed them and special services would still have to be provided. APTA challenged the regulations in federal district court here and lost.

The transportation regulations stemmed from Section 504 of the Rehabilitation Act of 1973, which provides, in part: "No otherwise qualified handicapped individual . . . shall, solely by reason of his handicap be denied the benefits of . . . any program or activity receiving federal financial assistance . . ."

New buses and new subway systems are built with 80 percent federal aid.

The Public Works Committee amendment would permit localities to set up alternative transit service for their handicapped residents. The alternatives would have to be approved by the secretary of transportation, would be eligible for federal aid, would have to charge the same fares as the regular public transit system and would have to operate the same hours.

Such alternatives -- probably a fleet of special vans -- would save the cost of refitting old subway systems and equipping new buses with wheelchair lifts. Such lifts have proved highly unreliable in Washington and elsewhere, in addition to costing about $20,000 each.

The debate yesterday was primarily on the question of whether the amendement would force the public transit authorization bill into a procedural fight with the Education and Labor Committee, which wrote the original Section 504.

Rep. James J. Howard (D-N.J.), chairman of the surface transportation subcommittee, said he had been assured by the House parliamentarian that no Labor Committee action was necessary. The amendment survived, 29 to 6, as several wheelchair-bound observers crowded the aisles of the packed committee room.

"There is one benefit," said George Conn, legislative director for the Paralyzed Veterans of America. "This action will galvanize disabled people in a way you have never seen before."

The authorization bill is $3 billion higher than the Carter administration figure and $3 billion more than is contained in a similar bill that passed committee in the Senate Tuesday. The Senate bill does not contain the section allowing local option on handicapped services.

Transportation Secretary Neil Goldschmidt, in a letter to the Public Works Committee, opposed both the funding levels and the local-option provision.