A staff psychiatrist at St. Elizabeths Hospital, Dr. Walter M. Presnell, has resigned his $64,764-a-year position amid an investigation by the hospital of allegations he engaged in homosexual sex with and furnished marijuana and alcohol to some patients he treated in the Boston area in the 1970s, a hospital spokesman said yesterday.

Spokesman Harold Thomas said Presnell, who was hired by St. Elizabeths in October 1979, quit his post on Sept. 17. Thomas said the reason for Presnell's resignation was a confidential personnel matter. Presnell, who earlier denied the allegations, could not be reached yesterday for comment.

A few days after Presnell's resignation, medical licensing authorities in Connecticut ordered a Nov. 5 hearing to investigate 25 formal allegations of malpractice involving Presnell's professional conduct in Lynn, Mass., near Boston.

Presnell held a Connecticut physician's license at the time, according to officials.

According to the allegations, made public yesterday by the Connecticut Department of Health Services in Hartford, Presnell furnished drinks and marijuana to some patients during therapy sessions and had sex with or made sexual advances to five male patients in his office.

St. Elizabeths placed Presnell on administrative leave in June after The Washington Post reported that three insurance companies had agreed to a $225,000 out-of-court payment to settle a lawsuit in federal court in Boston filed against Presnell by one of the former patients.

Presnell later returned to work at the federally owned mental hospital in Southeast, but was not permitted to deal directly with patients, according to spokesman Thomas. Thomas said the hospital's investigation of the allegations was incomplete when Presnell quit.

Besides Connecticut, the Georgia State Board of Medical Examiners has said it, too, will order a hearing on the same allegations because Presnell is licensed to practice medicine in that state. Presnell, who is not licensed in the District, practiced at St. Elizabeths under the aegis of his Georgia license.

Connecticut health service officials said yesterday that Presnell's license there has lapsed. But Dr. Henry Mannix Jr., chairman of the state's medical examining board, said the board is empowered to revoke or suspend a physician's practicing privileges, even if the certificate has been surrendered or is no longer current.

"The point of it is to try to prevent a physician from jumping from one state to another who's a bad actor," Mannix said. He said sanctions are reported within 30 days to the National Federation of State Medical Boards in Fort Worth, a clearinghouse for such information.

Action against Presnell in Connecticut, if any, could range from revocation to a suspension to a reprimand, Mannix said.

According to sworn statements taken in the Boston lawsuit, Presnell was employed at Undercliff State Hospital in Meriden, Conn., from Nov. 2, 1965, until mid-1968, when he left for the Boston area.