The Veterans Administration, operator of the nation's largest medical system, cost the government $34.5 million in medical malpractice claims in fiscal 1983 and 1984, according to an internal report.

An audit by the VA's inspector general's office said the money was paid for settlements and judgments, and that $2.3 million more is paid annually in VA compensation for injuries inflicted during VA medical treatment.

The final report of the inspector general's audit of medical malpractice claims was released last week in response to a Freedom of Information Act request by The Associated Press.

The VA, whose medical system is the largest in the nation, treated more than 36 million patients during those two years, and during that period, 1,671 malpractice claims and 550 malpractice suits were filed against the agency.

"No conclusions can or should be drawn from the malpractice data presented in this report regarding the relative incidence of malpractice in the VA, or the quality of care provided by the VA," the report said.

VA Administrator Harry N. Walters said in a written statement he is "concerned that some of the findings in the report could be taken out of context and could unduly and unnecessarily alarm veteran patients."

Walters said that, since the audit was begun a year ago, the agency has begun a program to improve patient monitoring and is developing ways to monitor the supervision of surgical residents.

The audit said there were 1,278 claims against the agency and 432 lawsuits that were settled during that period, with money paid in 35 percent of the cases.

No figures were available for malpractice payments for the most recent fiscal year, but the inspector general said the annual figure is expected to be even higher. Two cases alone in 1985 have resulted in $5.3 million in payments.

The inspector general's office recommended a number of policy changes, saying the agency conducted no in-depth analysis of the causes of malpractice cases. VA officials concurred with most.

The audit said the VA's system of reporting patient incidents was inconsistent and that the agency had identified only 18 percent of the injuries to patients that resulted in claims.