The Smithsonian Institution, which earlier this summer was cited for nearly 40 violations of federal regulations governing cancer-causing PCBs, has taken steps to rectify the violations and should be in compliance by the end of the month, the U.S. Environmental Protection Agency reported yesterday.

On Wednesday the EPA reinspected PCB transformers in three museums where violations were found in July, and repairs are "proceeding at a reasonable rate," EPA spokesman Harold Yates said. He said the agency will inspect the transformers for a final time in about a month.

The EPA inspections were prompted by reports that many of the Smithsonian's 57 transformers cooled by PCBs (polychlorinated biphenyls) were leaking the fluid, a known carcinogen that becomes 1,000 times more deadly when it catches fire. The leaks were discovered during a June 27 visit to the Smithsonian by the D.C. Fire Department's Hazardous Materials Unit.

Smithsonian officials said last week that they will ask the federal government for $3.5 million to replace or decontaminate their PCB transformers by Oct. 1, 1990, by which time all high-voltage PCB transformers will have to be phased out of use, according to EPA regulations. In the meantime, the officials said, about $360,000 is being spent on emergency work on transformers and other electrical equipment.

Last Saturday, officials of the American Federation of Government Employees Local 2463, which represents electrical and other workers at the Smithsonian, asked the National Institute for Occupational Safety and Health to conduct a health hazard evaluation of the institution.

In the request form sent to NIOSH, the union cited "unreasonable fire hazards resulting from faulty electrical systems . . . inadequate manpower to assure compliance with EPA directives and regulations, absence of a prepared plan of action to comply with all EPA directives and regulations and inadequate safety clothing" for employes.

A spokesman for NIOSH said an evaluation inspection probably would not be scheduled for at least a month.

In the first EPA inspection on July 19, the agency found violations in the use, disposal, marking, storage and record-keeping requirements for PCBs. Leaks were discovered in 25 transformers in the Museum of Natural History, the Museum of American History and the National Portrait Gallery/Museum of American Art.

EPA spokesman Yates said that Wednesday's inspection of transformers in the same buildings uncovered another leak in a PCB transformer that was not previously inspected. He said the leak is being repaired.

When the repairs are completed, Yates said, the Smithsonian will file a report stating that the cleanup is finished and the transformers are secure, after which the EPA will conduct a final, "less detailed" inspection. "At this point we are satisfied that the Smithsonian will bring itself into compliance," he said.