The federal Office of Management and Budget has rejected a special $642,731 reimbursement sought by the District of Columbia to pay the cost of Pope John Paul II's visit here, forcing the financially strapped city to pick up the bill itself.

Mayor Marion Barry disclosed the OMB decision in a letter delivered yesterday to the City Council. Barry said he plans to delay a $2 million payment to the U.S. Bureau of Prisons and expects instead to spend the money to meet other expenses, including overtime pay for police called to duty for the papal visit last Oct. 5-7.

Barry's letter accompanied a revised version of his proposed request to Congress for a supplemental appropriation of $62 million for the current 1980 fiscal year. If granted, that supplement would push the total 1980 federal payment to the city to $300 million, the maximum allowed under the city's charter. The council must first approve the request before it is sent to OMB and then to Congress.

The request for supplemental funds is a key part of Barry's program to avert a deficit projected as high as $172 million. Barry also has announced $23 million in cutbacks in city operations and a plan to increase taxes and fees by $24 million this fiscal year.

Barry submitted his supplemental proposals as he prepared to testify today before the House District Appropriations subcommittee in his first public appearance on Capitol Hill since the city's financial crisis came to light in January. His testimony will deal chiefly with the budget of fiscal 1981, which starts Oct. 1, but the city's current problems seem sure to come up.

The mayor's proposed changes in this year's supplemental appropriations arrived as the City Council, sitting as a budget committee, was preparing to vote on the original version proposed by Barry on March 6. The last-minute change angered some council members, with Jerry A. Moore Jr. (R-At Large) accusing the mayor of dealing with the budget in a piece-meal manner.

In the total dollar amounts, Barry's two versions of the supplemental are identical, but the decision to delay the $2 million payment to the Bureau of Prisons for housing District prisoners until after Oct. 1 permitted the mayor to propose the use of those funds for other city operations that are caught in the budget squeeze.

Amoung the funds that Barry wants Congress to appropriate as part of the remaining federal payment is $362,000 to pay some of the expense of police overtime at the papal visit. The police department and other agencies would be forced to absorb the remaining $280,000 from money already appropriated to them.

Under the congressionally enacted Home Rule Act, the U.S. government is directed to reimburse the city "for necessary expenses incurred by the District in connection with assemblatures . . . which relate primarily to the federal government." Such payments are in addition to the regular federal payment.

Barry said the city thought the pope's visit should qualify, but OMB officials sent word last week that "they would not entertain a request" for such funds.

D.C. Budget Director Gladys Mack said the city also dropped a related request for $86,000 to pay the costs, mainly of police overtime, in dealing with a demonstration Dec. 1 by Iranian students seeking a return of the deposed shah to Iran.

The mayor also requested $683,000 for pay raises that the Corrections Department cannot absorb in its budget. Mack said this would make no change in the requirement that the department lay off 360 employes as an economy move. i

At yesterday's meeting, the council members voted preliminary approval of Barry's first version of the supplemental request after making some changes in the distribution of the funds while keeping the dollar total unchanged. The council will consider both versions when it meets tomorrow for a final vote.

A controversy erupted yesterday over Barry's proposal to ask Congress to ratify a $6.1 million reduction in the current school board budget as part of his cost-cutting program.

Hilda Mason (Statehood-At Large), a former school board member, moved to take that reduction out of the pending bill. Lost 10 to 3, with her only support coming from Betty Ann Kane (D-At Large), also a former school board member, and Wilhelmina J. Rolark (D-Ward 8).

Both Barry's and the council's revised version of the supplemental bill provide, in procedurally different ways, for $4.1 million to pay for wage increases already granted to school employes. The council version added $815,000 to provide tuition grants for special education of handicapped pupils. $8

The council approved a proposal by its Human Services Commission to shift $1.3 million into the city's general public assistance program, reducing the Department of Human Services oil-heating budget by a like amount. It also approved a proposal by the Judiciary Committee to reduce by $140,000 the police department's request for a $400,000 supplemental outlay for gasoline.