Bethesda Naval Hospital is shutting down its training program for cardiothoracic surgeons because no one there is certified to head the 21-year-old program, the hospital's commanding officer said yesterday.

The decision to close the program comes a year after Navy Cmdr. Donal M. Billig, former head of the cardiothoracic unit and the program director, was first investigated on questions of competence.

In June, Billig was recommended for a general court-martial and charged with involuntary manslaughter of five patients and with dereliction of duty in connection with operations he performed at Bethesda.

The hospital's commanding officer, Navy Capt. Stephen Amis, whose initial inquiries prompted the Billig investigation, testified yesterday in a preliminary hearing for Billig that he had decided to close the training program by Dec. 31 because no doctors there are certified by the American Board of Thoracic Surgeons. Staff surgeons operating in the cardiothoracic unit at Bethesda have been certified in general surgery, he said, and will continue to perform heart surgery.

Bethesda had attempted to fill the position formerly held by Billig with the appointment of Army Col. Michael Barry, the former assistant chief of cardiothoracic surgery at Letterman Medical Center in San Francisco. Barry was assigned to Bethesda July 1 and given temporary privileges for three months.

Comments from other doctors at Bethesda alleging that Barry "handled tissue roughly" led Navy officials there to request that Barry undergo another three-month trial period. Barry declined and was reassigned to Walter Reed Medical Center.

"I think that I at Bethesda and my senior medical officers had become supersensitized" to the operations of the cardiothoracic unit, Amis said to explain the concern over Barry. But the decision to deny full privileges to Barry, who is certified in both general and cardiothoracic surgery, also meant the hospital would have to make another choice, he said later.

"Losing the second head of cardiothoracic surgery within a year, I knew we would be looked at very askance as far as accrediting the program and I elected instead to terminate it," Amis said. Training programs must be approved by an accrediting council of the American Medical Association. Bethesda, one of four teaching hospitals in the Navy, had had 17 teaching programs for residents. The cardiothoracic program, begun in 1964, was designed as a two-year program of study and work.

Amis' statements yesterday were part of a reopened investigation to determine whether Billig should face a court-martial based on charges stemming from the deaths of the five patients. Amis said yesterday that he began having concerns about Billig in November 1984 when Bethesda officials began monitoring the number of deaths and complications stemming from each surgeon's operations.

"In one day, I spoke to six surgeons and one resident and I could find no one who had kind words to say about the techniques of Cmdr. Billig," said Amis, who then was the executive officer, the second-highest official, at the hospital.