The federal government lost billions of dollars this year because of poor management in virtually every major agency, the General Accounting Office concluded this week.

In a year-end report card that credits the administration with good intentions but poor follow-through, the GAO found significant breakdowns in weapons procurement, Social Security administration, property management and almost every other governmental function involving large sums of money. Although each department has pledged improvements, the GAO said, "the major problems so far remain largely unchanged."

"Widespread and often longstanding weaknesses and breakdowns in agency internal controls continue to result in wasteful spending, poor management and losses involving billions of dollars of federal funds," Charles A. Bowsher, comptroller general and head of the GAO, wrote in a letter presenting the report to Congress. "The weaknesses have also made outright fraud more feasible."

The GAO, Congress' investigative arm, examined 23 agencies that together spend more than 95 percent of the federal budget. It found that none of them has fully implemented the Federal Managers' Financial Integrity Act of 1982, which was meant to improve internal financial controls in federal bureaucracies and bring some consistency to the 427 separate accounting systems that they use. (The Defense Department alone uses 150.)

The Office of Management and Budget, which is responsible for implementing the act, responded to the GAO report by claiming "considerable progress" in implementation. Joseph R. Wright Jr., deputy OMB director, said that improving financial management is a top administration objective but cautioned that the GAO's calls for closer monitoring of agency progress could backfire.

"We are concerned that complying with the GAO recommendations would impose an audit-oriented approach, require much more detailed testing and result in cumbersome reporting and even more paper work," Wright said in a Nov. 25 letter to Bowsher.

Many of the problems cited in the GAO report have been reported previously, either by the GAO or by inspectors general. Taken together, they portray a system with such poor controls that it often cannot tell how much money is seeping away:

*The Treasury Department's computer systems are vulnerable to accidental or intentional misuse, the GAO found. The result is "continued potential for fraudulent diversion of electronic funds transfers totaling billions of dollars."

*The Veterans Administration wastes millions of dollars by failing to control medically unnecessary admissions, according to the 71-page report. In addition, the VA maintains such poor watch over drug supplies that "it was very difficult to determine whether a particular drug was missing, or in cases where VA could tell what quantity was missing, how it disappeared."

*The Defense Logistics Agency, which buys supplies for the military, reported last year that it had paid $22.6 million for items that it could not verify had been received. Another $53 million had been spent for products that were already 90 days past delivery at the time of the GAO review.

*Immigration records in the Justice Department's Immigration and Naturalization Service were "vulnerable to alteration," the GAO found. "Over the past three years," the report says, "more than 100 employes have been charged with fraudulently altering alien registration records and/or accepting bribes, and 17 have been convicted."

*The GAO said the Pentagon procurement system, which will spend $100 billion this year, continues to be marked by weak controls leading to overpriced spare parts, lack of competition, cost growth and a reliance on contractor cost estimates.

*In an echo of those familiar problems, the GAO said, the National Aeronautics and Space Administration does a poor job of buying spare parts for its space shuttle, which are expected to cost $2.3 billion through 1994.