NEW YORK, AUG. 2 -- The government today indicted Rep. Floyd H. Flake (D-N.Y.), pastor of a church in his Queens district, on charges of embezzling funds from a federally subsidized senior citizens housing project that his church built and operated.

Flake, elected in 1986, was charged with 17 counts of conspiracy, fraud and tax evasion in the indictment announced by U.S. Attorney Andrew J. Maloney. It also lists seven counts against Flake's wife, Margarett, described as the bookkeeper in the operation.

As pastor of the powerful, 6,000-member Allen African Methodist Church, Flake served as chairman of the Allen Senior Citizens Apartments, a 300-unit housing complex built with a $10 million loan from the Department of Housing and Urban Development. HUD also provides $100,000 in monthly subsidies to operate the complex.

The Flakes are charged with stealing $75,000 in HUD funds between 1983 and 1987 by billing the Allen Apartments for transportation supposedly provided by the church, and then pocketing most of the payments.

Flake and his wife are also accused of diverting $66,700 in church funds into bank accounts established allegedly to disguise income that they failed to report to the Internal Revenue Service.

In announcing the results of the 18-month investigation, Maloney said, "The defendent's conduct deprived the senior citizens, whom they were pledged to protect, of the federal funds specifically designated for their care."

Flake did not respond to telephone calls today, but in a statement released this morning before the indictment was announced, he denied any wrongdoing. "The prosecutor is attempting to substitute his judgment on how a church should manage its affairs and how a pastor should fulfill his special duties in an inner city minority community," he said.

Flake said he was particularly disturbed at the charges against his wife. "She had little to do with the housing project or preparing our tax returns," he said.

Highly publicized charges of sexual harassment surfaced against Flake more than two years ago. Thelma Singleton-Scott, his former executive assistant at the church, is suing Flake on charges he harassed her into leaving her job after she ended a two-year affair with him. Flake serves on the House committees on Small Business; Banking, Finance and Urban Affairs, and the Select Committee on Hunger.

If convicted on all 17 counts, he could be sentenced to a maximum of 87 years in prison and fined up to $3.95 million. Margarett Flake faces penalties of 55 years in prison and up to $2.1 million in fines.