A long-awaited General Accounting Office report has sharply criticized the Agriculture Department for spotty enforcement of the Animal Welfare Act, which is designed to protect animals housed in zoos, kennels, research facilities and traveling circuses.

Some animal shelters are rarely, if ever, inspected, according to the report released last week. Most investigators are trained on the job, and when problems are found, such as cramped kennels or dirty cages, inspectors often don't follow up to see if the problems have been corrected.

The report, however, does not address one central question: does the lax enforcement mean more money is needed, as animal welfare advocates have urged, or does it mean the program should be eliminated, as the Reagan administration has suggested?

The administration has contended that states and local humane groups are in a better position to deal with the problem. White House officials have found some support for that view in the Agriculture Department, whose inspectors are used to fighting disease in domestic farm animals rather than policing "puppy mills" and circuses.

But the very vocal critics in the animal welfare community insist that the protection of animals' rights should be left to Washington.

"There are very few states with [animal welfare] laws on the books right now," said Yvonne Eider, legislative director for the Friends of Animals. "And what authority do the humane groups have, short of breaking into labs -- and that's illegal."

The report by the congressional watchdog agency concluded, "The ultimate decisions as to the extent of the federal role in animal welfare enforcement and the appropriate level of funding for the federal role will have to be made by Congress."

Congress is likely to compromise by continuing to fund the program, but only at the current level, according to knowledgeable staffers. "Most of the groups will be satisfied if we just fund the program at the current level," said one Capitol Hill aide, who asked not to be quoted by name.

"It's just a low priority for this administration," the staffer said.

The report found that the department's inspections of research labs and kennels varied widely in the six states that were surveyed. Inspections averaged about two a year for facilities in Iowa and Kansas, but less than once a year for those in California.

About half of the facilities in California and New York were never inspected, the report found.

Unannounced inspections are the department's principal tool for making sure facilities comply with strict federal standards regarding cleanliness, cage size and animals' well-being. The GAO said that four inspections per year for each facility would be optimum, based on interviews with Agriculture personnel.

"It's really about what I expected," Eider said. "There really has been nothing there for the money."

Dr. Richard Rissler, assistant director of USDA's animal health programs, disagreed. He said the department was well aware of the problems cited and has already moved to remedy most of them.

"Most of what they uncovered we are aware of and are either correcting or are in the process of correcting," Rissler said. He said the GAO was using some old data, gathered before many of the reforms took hold.

For one, Rissler said, the department decided a year ago that an average of two inspections per facility per year was more than adequate, with some highly reputable facilities receiving less attention. "It was really a waste of time in some cases" to continually inspect, he said. "It was really not the most efficient use of manpower."

Rissler also said three new national training courses have been established: for inspectors of research facilities, for general inspectors and for inspectors of marine mammal facilities.