Air Force medical commanders let a heart surgeon continue to operate on patients without a full investigation after his competence had been questioned by his fellow doctors, according to a report forwarded yesterday to Secretary of Defense Caspar W. Weinberger.

The report said medical officers failed to live up to their responsibilities and a "significant systems failure" occurred when the Air Force failed to evaluate the doctor throroughly after nearly half his patients died during a 17-month period, according to congressional testimony.

A conflicting study made by five military doctors, and released by the Air Force yesterday, defended the surgeon, saying the mortality rate for his operations in the questioned period was only 22 percent and the patients who died were largely high-risk ones with little chance for life.

The higher figures were given to a congressional subcommittee by Dr. John Beary, acting assistant secretary of defense for health affairs, who said "you would expect" about a 13 percent death rate in such cases, "and that is generous."

Yesterday's Defense Department report questioned the validity of the Air Force's figures.

Despite some reforms since the incident, the report urged Weinberger to order an evaluation throughout the armed forces of the medical care given the military, their families and retirees "to ensure" that a similar incident "is foreclosed forever."

The disputed case is that of Dr. William Stanford, now retired as an Air Force colonel, whose operating skill at Wilford Hall Hospital in San Antonio, the Air Force's largest and most prestigious medical institution, was questioned by fellow doctors in 1977.

Stanford's then-commanding officer, Paul W. Myers, then a brigadier general, supported him and approved training for him at a Milwaukee civilian hospital without revealing his disputed record.

The stinging Defense Department report was made by Dr. Theodore Cooper, executive vice president of the Upjohn Co. and former assistant secretary for health in the old Department of Health, Education and Welfare, and Joseph H. Sherick, Weinberger's assistant for review and oversight.

Cooper and Sherick did not pass judgment on Stanford's surgery, but on Air Force failure to "resolve" his competence, despite later investigations. Cooper and Sherick noted that the civilian Society of Thoracic Surgeons is studying Stanford's record at Air Force request.

Stanford, now a University of Iowa radiology trainee, said yesterday that the new Air Force report bears out "what I was claiming all along, that the [Wilford Hall mortality] figures were perfectly acceptable, and that the cases were the hard, difficult cases that I was assigning myself."

The Cooper-Sherick report also said the surgeon's immediate commanding officer, Myers--who was soon to be named Air Force surgeon general--"fell short" of meeting his responsibilities in evaluating Stanford or limiting the scope of his surgery pending thorough study.

Myers retired as surgeon general last summer, but was kept on duty by Weinberger pending yesterday's report. Myers is expected to retire shortly with the rank of lieutenant general, a rank that carries two more stars than brigadier.