Elliot Siegel, one of the most powerful backstage figures in the musical life of Washington, has resigned from two key positions and has said he left uncashed checks destined for a musicians' union pension fund sitting in a drawer for months.

One local member of the musicians' union complained to the Labor Department, which has opened an investigation.

Siegel, a violinist, has tenure in the Kennedy Center Opera House Orchestra but resigned Tuesday as its leader and personnel manager. A week ago, he resigned as orchestral contractor for Kennedy Center Productions.

Siegel said last week there were some late payments to the pension fund, and that they were an "honest oversight."

Stephen Pine, a Labor Department official in New York, said a case had been opened on the American Federation of Musicians' welfare fund to which Siegel was supposed to have been making payments on behalf of the musicians. Pine would not discuss details of the case.

As a contractor, Siegel recraited orchestral players for opera ballet and special occasions at the Kennedy Center and Wolf Trap. He also was responsible for transmitting dues to the union and retirement payments to the musicians' pension fund in New York.

Concern about pension fund payments began earlier this year when a violinist in the orchestra checked her retirement credits on printouts routinely sent to her by the pension fund, and found them "extraordinarily low." She complained to the union and also told other members of the orchestra, who began checking their own records and finding discrepancies. Walter Salb, a drummer, orchestra leader and contractor, complained to the Labor Department. Salb is a member of the local musicians' union. He is not a member of the Kennedy Center orchestra and was not affected by the pension fund payments in question.

Siegel has made two pension fund payments -- one of approximately $45.000 and another of $67,500 -- as back payments. One such payment was reportedly made in August of this year, another in June 1981.

Siegel said he was responsible for delays of up to eight or 10 months in pension payments and confirmed the essential accuracy of the figures. "Running an orchestra is a very complicated business," he said. "It was just too much work for one person to handle with all the paperwork. I guess I needed a secretary."

He said the payments in question were "Kennedy Center checks made out to Local 161-710 of the AF of M [American Federation of Musicians] and the AFM and EPW Fund [the pension office in New York]. My job was essentially to take the checks to the union local; there was nothing else anyone could do with them. Sometimes in the press of other things to do, it just got bypassed; it just happened. But the checks I handed in were the original Kennedy Center checks; I didn't do anything with that money except to leave it lying in a drawer for a long time. Wolf Trap sent their own checks to the union, so that took some work off my hands."

The situation is more complicated in relation to the Washington Opera, for which Siegel also handled the musicians' payroll. He would receive a lump-sum check and make out paychecks to the musicians from an account under his control. While the salary checks were always given out promptly, he said, the dues and pension part of the money would sometimes pile up in the account for months. He said he recently made one payment of approximately $15,000 to the fund out of this account and will make a final payment of about $17,000 in November.

Officials at Wolf Trap said they had no problems with Siegel's work. "He's been with with us for more than 10 years," said Ann McKee, director of production at Wolf Trap, "and he's provided us with glorious orchestras, but more than that he's been a real friend to Wolf Trap. I'm willing to stand baside him, and I expect him to continue working for Wolf Trap for many years."

Officials for both the Washington Opera and the Kennedy Center said that normal procedures had been followed by their offices throughout the period in question. "We're still in the dark about a lot of details," said Martin Feinstein, general director of the Washington Opera. "I hope it's just a bookkeeping foul-up."

"Siegel has resigned, and we are looking for another contractor," said Thomas R. Kendrick, director of operations at the Kennedy Center. He reported that at least eight checks for the pension fund had been given to Siegel and had not been cashed. Until a new orchestral contractor is found, he said, violinist and contractor Eugene Dreyer (who currently contracts orchestras for musical comedy at the Kennedy Center) will take over Siegel's former functions.