The American Civil Liberties Union charged yesterday that the Navy has begun discharge proceedings against 16 women after female sailors aboard the missile ship USS Norton were asked to check off names of suspected lesbians on a ship's roster.

Lt. Cmdr. Mark Baker of the U.S. Pacific Fleet immediately denied the charge. "There was no list circulated," he said. "The investigation began when a female crew member reported allegations to her commanding officer."

Susan McGreivy, an ACLU staff attorney in Los Angeles who is representing the sailors, said the ACLU will seek a federal court order within the next few days to halt the discharge procedures against the women, who are still working on the ship.

The case promises to focus renewed attention on the controversy over whether homosexuals should be dismissed from the armed services, as well as the methods used to identify them. Studies estimate that 10 percent of the military is homosexual, despite regulations requiring discharge of anyone engaging in a homosexual act or exhibiting homosexual tendencies.

Baker said 24 women aboard the USS Norton were originally being investigated, but eight were cleared. "The investigation which began on May 15 is still in progress," he said. "No charges have been filed against any individual. Administrative examination of the allegations is continuing." a

McGreivy said the women received notices June 4 that they were being processed for discharge because of "unsuitability based on homosexual acts." Baker said he was unaware of any such notices.

McGreivy said a woman sailor aboard the Norton had told at least three of the sailors under investigation that she was asked to check off names of suspected lesbians with a red pencil. There were other red pencil checks already on the list, McGreivy said.

"This is a disgusting witch hunt," she said. "There is no offering of proof any of these women are lesbians. They have not been told who their accusers are . . .

"It boils down to character assassination. Some petty officers might have hostility against you or may think that the way people look makes them gay. This gives the Navy the right to dismiss people based on hearsay." t

Sixty-one women, including three female officers, are stationed on the Norton, based in Port Hueneme, Calif. The ship is one of seven Navy ships in the "women at sea" program begun two years ago.

Also aboard the ship, which is docked at Long Beach for maintenance, are 298 males, including 16 officers. No investigation for male homosexuality on board was undertaken, Baker said.

The 16 women under investigation range in age from 18 to 35 years old, in rank from seaman first class to petty officer and in occupation from engineer to radioman and quartermaster, McGreivy said.

Thirteen were taken to the Long Beach base hospital Monday and were given psychiatric evaluations by health workers untrained in psychiatry. The examinations lasted less than 10 minutes each, McGreivy said. "It was mass production on a grand scale. The Navy panicked," she said.

Although McGreivy said the women were told by a Navy officer that they could have no hearing because they would receive honorable discharges, Baker said they would have a right to a hearing before an administrative board.

"Some of these women, are outstanding sailors," McGreivy said. "They have collectively over 70 years of military training and service. Now their careers are being ruined."

A Navy spokesman said 842 persons were discharged in 1979 for homosexual acts or tendencies.

The ACLU also defended Sgt. Leonard Matlovich, who filed suit in 1975 when he was dismissed by the Air Force for homosexuality. Matlovich had a spotless record and served three tours of duty in Vietnam. His case is pending before U.S. District Court Judge Gerhard Gesell.

The Navy policy outlined in official instructions is: "Any member who solicits, attempts, or engages in homosexual arts shall normally be separated from the naval service. The presence of such a member in a military environment seriously impairs combat readiness, efficiency, security and morale."