Richard C. Siegel, the budget director for the D.C. City Council and a top aide to Council Chairman David A. Clarke, has been appointed the city's acting budget director by Mayor Marion Barry, the mayor announced yesterday.

Siegel, who worked as a budget and financial official for the Barry administration before taking the council post in 1983, is expected to bring stability and expertise to the important budget job, which has been vacant since Betsy Reveal resigned last fall. The post took on added importance with the resignation a week ago of Alphonse G. Hill, deputy mayor for finance, whose duties included supervising the District's nearly $2.7 billion-a-year budget.

Clarke and other council members praised the selection of Siegel, but said they were stunned by the decision, which comes at a time when Clarke is considering challenging Barry for the mayoralty this year.

Clarke said he was unaware that Siegel was under consideration for the job until a reporter informed him Monday night.

"It's a way of upstaging Dave," said one council member, who asked not to be identified. "At a time he is considering running for mayor, the mayor comes along and hires Dave's budget director."

But aides to Barry insisted that politics had nothing to do with the decision.

"The mayor was looking for a person . . . who could hit the ground running," said one of the aides. "Who knows the financial management system better than Rich Siegel . . . . The decision had nothing to do with getting at Dave Clarke. That was the least of the mayor's concerns."

Clarke also said he did not think Barry's move was politically motivated. However, he said he was upset that Siegel, the council's top budgetary staff member, was negotiating with the administration at the same time that the council was reviewing the mayor's proposed fiscal 1987 budget, which the council approved last week.

"That's not something that is done within the legal profession or in other adversial roles," Clarke said.

"It doesn't surprise me what the mayor did, but I would have expected a little bit more from Rich," said Clarke, who is also a longtime friend and neighbor of Siegel's.

A top Barry aide, who described the negotiations leading to Siegel's appointment as "tender," said Barry had planned to talk with Clarke about the matter later this week before it was to be made public. But the plan fell apart when word of the appointment leaked out. The aide said both Siegel and Barry had been concerned about preserving the integrity of the council's budget review process.

Siegel said he was embarrassed that Clarke learned the news from a reporter. "I've known Dave for 12 years. I have a tremendous respect for him. I know this is hurting him very much. But it's a tremendous opportunity for my career. I want to serve the city."

As council budget director, Siegel supervised a staff of two and received a salary of $57,475 a year. As the city's budget director, Siegel's salary is expected to be $65,930 a year and he will supervise more than 50 employes.

Siegel said he had been looking for a new job for months and when Reveal left government last September to take a job at Harvard University, he let it be known that he was interested in replacing her. He said serious discussions took place in recent weeks. His appointment as acting director becomes effective April 14. A final decision on the post will be made after this fall's elections.

Siegel, 40, a Boston native, worked for the University of the District of Columbia before joining the Barry administration in October 1979. He played a key role in overseeing the early development of the city's financial management system and was deputy director of financial information services when he resigned to take the council post in January 1983.