Mayor Marion Barry, citing the city's budget crisis, has warned that more than 35,000 District of Columbia government employes may not get pay increases on Oct. 1, the beginning of the new fiscal year.

The threat was disclosed at a meeting of the D.C. City Council, which voted tentatively to give the mayor power to withhold higher wages normally tied to the annual salary increases for federal employment that city workers have come to expect. A final vote is expected in two weeks.

"Because of the uncertainties about the status of our fiscal year 1981 budget request, which has not yet been acted upon by Congress," the mayor wrote the Council, "I am at this time proposing no changes in pay for city workers . . ."

The mayor's letter came at a time when the city faces a cash deficit of $60 million to $100 million in the current fiscal year and is seeking ways to overcome a deficit accumulated from past years that Barry has said totals $284 million.

Barry has scheduled a 15-minute broadcast on three television stations next Monday evening to announce his plan to eliminate the deficit and offer his proposals to solve the financial crisis.

Union leaders, told of the mayor's warning, voiced doubt the pay freeze would happen.

"We will fully expect a pay raise," declared Larry Melton, local vice president of the International Brotherhood of Police Officers.

Donald MacIntyre, regional vice president of the American Federation of Government Employes, which represents 9,000 city workers, said the union would go to court to challenge any failure of the city to pay increases that union members regard as their right. Representatives of other city employe unions could not be reached for comment yesterday.

Until last year, under a procedure that was almost automatic, District employes received the same percentage pay increase the president granted to federal workers. But new procedures for setting wages of most District employes by collective bargaining between union and city represenatatives went into effect this year.

Union and some city officials said yesterday, however, that the procedure for bargaining has not been fully established, dumping the issue of this year's pay raise into the lap of the mayor.

Technically, under the new city personnel law, the mayor can set the pay only for a small group of high-level career employes who are not members of unions. But some insiders expect he will have to set the scales for everyone this year.

President Carter, in the federal budget he submitted to Congress in January, proposed enough money to give all U.S. workers a pay increase of up to 6.25 percent. The actual amount will not be known until at least the end of next month.

However, the D.C. City Council, in sending the city's proposed amended budget for the 1981 fiscal year to Congress last month, proposed spending only enough money to grant a maximum increase of 4.8 percent to city employes.

The money to finance the $25 million for pay increases is in jeopardy, Councilman John A. Wilson (D-Ward 2) said yesterday, because the latest official forecast for city tax collections has been reduced by $22 million.

The House District Appropriations subcommittee, the congressional panel that usually acts first on the city budget, has postponed action on its version of the city's spending program until after it returns from a recess next Monday. Barry, however, was required to submit his recommendations for a city pay increase by July 1.

Even before issuing his warning that surfaced yesterday, city officials discovered that the wording of the District's old personnel law apparently required the city to match the federal wage increase -- at whatever level it was set by the president -- for all municipal employes on the payroll before Jan. 1, 1980.

Barry asked the council to enact legislation making clear that the city has full power to grant wage increases below the federal level to all of its employes, whether or not they were working for the city before that date.

MacIntyre, the American Federation of Government Employees official, said that would violate the city's new personnel law, which assured all employes previously on the payroll that they would not lose any pay or benefits as a result of shifting to the new personnel system.

"I don't think the mayor has any choice but to give incumbent [long-time] employes what the federal employes will get on Oct. 1," he said.

Melton, the police union official, said police and firefighters' union negotiators are preparing to begin negotiations with city officials regardless of the mayor's warning. Police and firefighter wages, by law, are supposed to be set by negotiation, but in practice the uniformed employes in recent years have received the same pay as federal and other District workers.

A major hitch that has locked negotiations has been a delay in establishing the bargaining units for negotiations by the city's new Public Employe Relations Board. A spokesman said about 4,000 of the city employes are members of 14 unions, many of them small.

The Council approved yesterday the legislation sought by Barry with only one audible dissenting vote, by Wilhelmina J. Rolark (D-Ward 8).

John A. Wilson (D-Ward 2), chairman of the Council's Finance and Revenue Committee, warned during debate that a failure to enact the bill would cost the city $47 million in additional wage costs that it does not have in its treasury and does not expect to receive.

Betty Ann Kane (D-At-Large) stressed that the legislation is designed to clarify the intent of the council in passing the new personnel bill that the city would no longer tie any of its salary scales to those of the federal government.

In contrast to the District's plight, government employes in most surrounding suburban jurisdictions have recently received annual pay raises, ranging from 5 percent in Prince George's County to 10 percent in Alexandria.

In other action yesterday, the council voted preliminary approval of a measure to extend the effectiveness of the city's existing rent control law from its scheduled expiration Sept. 30 until next April 30 to allow time for council action on a revised bill.