A federal grand injury here has begun an investigation of Dr. Murdock Head, the influential director of a Virginia foundation, who was accused in a court affidavit earlier this year of having made cash payments to members of Congress in return for their help in securing government contracts.

Sources close to the investigation have told The Washington Post that the investigation is in its "preliminary stages" and will take at least two to three months to complete. Head repeatedly has denied the charges made in the court affidavit.

FBI agents began an investigation of Head, who is also chairman of a George Washington University Medical Center department, shortly after an assistant U. S. attorney said in a court affidavit filed in Los Angeles that Stephen B. Elko, a former administrative assistant to Rep. Daniel J. Flood (D-Pa), made allegations of $87,000 in payments by Head.

The payments went to Elko, Flood and former Rep. Otto E. Passman (D-La.), according to the affidavit. Passman was indicted last week on charges of accepting $213,000 in cash from South Korean business Tongsun park in return for urginf sale of Louisiana rice to Korea through Park.

The Washington Post has reported that Elko has told government investigators that he received from Head cash gifts of $40,000 [WORD ILLEGIBLE] Elko also told investigators that his instructions from Head were to pass the money on to Flood and Passman. The monies allegedly were transmitted to Elko before an annual black-tie stag dinner which Head staged at his Warrenton, Va., farm between 1971 and 1973.

Head runs his organizations from an office in a restored Georgian mansion of the 1,700-acre Airlie Farm 50 miles west of Washington. The farm is the site of Head's movie-making operations as well as a large number of government agencies in Washington.

Spokesmen for Head, who holds graduate degrees in medicine, law and dentistry, and for GWU, where Head holds an endowed "Airlie chair," said yesterday that they knew nothing of the grand jury investigation. Head has previously asserted that he is innocent of the charges Elko has made.

Head and his staff have secured millions of dollars in federal contracts for movie-making and health information programs. SOme of the programs have won Head critical acclaim, including nine Emmys from the Washington chapter of the National Asociation of Television Arts and Sciences.

But some of the projects have also been attacked by internal government auditors and some government public affairs officials as costly and the products of intense congressional pressure.

Head has not denied that some of his backers have been among the most influential members of appropriations subcommittees in the health field. his organizations, he has said, have won the contracts on the basis of their reputations for excellence, not on the basis of his friendships.

Persons who have been interviewed by FBI agents who are investigating Head have said the agents' questions forcused on two areas: Heads's friendships with members of Congress and his contracts with the government.

In its first public comment on the controversy, GWU ackknowledged through a spokesman yesterday that the school's comptroller is conducting an "informal" investigation of Head's department. "There is nothing we can say about it," said GWU spokesman Jack Wilson.