A federal audit of the construction of a new Environmental Protection Agency laboratory in Annapolis says that contract supervision problems at the General Services Administration, mistakes by the builder and interference by the EPA may cost the government $1.5 million.

The audit by the inspector general of the GSA, the agency that provides office space for the federal government, says that "many of the building systems remain nonoperational 2 1/2 years after occupancy . . . . Even more striking is that GSA has inspected and approved full payment for incomplete work."

Records show that through the first two years GSA paid the Woodbridge Construction Corp., which built the water quality testing laboratory, $726,000. Woodbridge President A. John Briscuso denies that his company is to blame for any problems with the building.

The audit, conducted last fall and released this month, said that "a lack of adequate technical input in the conceptual, design and construction phases, has resulted in significant losses to the government."

"There are some rooms which we can't occupy, and we've moved laboratories to other rooms," said Orterio Villa, director of the lab. "The ideal way to do it would have been to complete the work before moving people in."

Most construction deficiencies turn up during routine inspections or when the government takes over the building, said Carl L. Brown, director of field audits for the GSA. "In this case," he said, "the problems existed more than two years after that point."

The 31,323-square-foot facility at 839 Bestgate Rd. was built by Woodbridge, an Annapolis-based company that primarily builds homes, under a lease-construction contract that was signed with GSA in 1977. Under that arrangement, Woodbridge owns the building and leases it to the government for 15 years.

The audit takes a swipe at the EPA for "causing administrative problems by making changes during construction without GSA's know-ledge and by purchasing equipment for the project which was not compatible with the buildings' systems." Villa said "a laboratory is like any business--your analytical equipment is always evolving, so there's no doubt that we changed some equipment. We were looking for better ways to do things."

Woodbridge President Briscuso said Thursday he was "shocked at the thought such problems exist." The building, he said, is "fully operational. This is the very first I've heard about any of this. How can I get a copy of that report? I want to know more."

The audit says Woodbridge failed to properly assess heating, cooling and ventilation system changes, costing the government $613,015; deleted work prescribed in the contract costing $104,567, and failed to perform work outlined in the contract costing $95,110. The auditors estimated that only 40 percent of the $1.1 million lost through March was "recoverable." However, James G. Whitlock, GSA regional public buildings commissioner, said the amount is subject to negotiations and could vary.

Additional losses over the life of the lease can be attributed to energy savings that "never materialized," the audit states, due to the installation of equipment suggested by the builder. The facility, the report says, is "one of the top energy users of any government-owned or -leased building."

"The major problem is with the heating, ventilation and air conditioning system," Villa said. "There's no humidity control for our sensitive experiments." Villa said that the agency's 30 employes are "making do."

"This is all amazing. There's absolutely no problem; they've all been corrected," Briscuso said. "The problems now emerging are the government's responsibility because they designed the building and what they didn't design they approved."