A two-year battle against the federal government ended in victory for a scientist fired from the Environmental Protection Agency after raising health concerns about fluoride.

Labor Secretary Robert B. Reich ordered that William L. Marcus be returned to his $ 87,000-a-year job at EPA and be paid back wages, legal costs and a $ 50,000 penalty.

“Fighting the federal government is by no means an easy task,” Marcus said.

Since being fired on May 13, 1992, he said, he has had to sell assets and depend on consulting work for income; one daughter had to postpone plans to go to medical school; vacations were no longer even considered and he and his wife both developed stress-related health problems.

Reich, in an order made public Thursday, upheld an earlier decision by Administrative Law Judge David Clarke Jr., which concluded that the EPA’s charges against Marcus were only “a pretext” and that Marcus actually was fired “because he publicly questioned and opposed EPA’s fluoride policy.”

EPA spokesman John Kasper said the agency would have no comment until the decision is reviewed.

Marcus was fired after a four-year investigation during which the agency accused him of improperly using agency information for private gain, being improperly absent from work and engaging in outside employment that appeared to pose a conflict of interest.

Marcus maintained that his EPA superiors knew about his outside work and that his dismissal actually stemmed from an internal memorandum he wrote in 1990 challenging the agency’s position on the health effects of fluoride. When the memorandum was leaked to the press, it caused embarrassment to senior EPA officials, Marcus argued.

Clarke wrote that after Marcus’ fluoride memo became public he had to submit weekly activity reports, lost his right to routinely engage in outside work and was restricted to “studying the least controversial chemicals.” He also was prohibited from taking part in questions involving fluoride, said Clarke.

In his ruling, Reich agreed with Clarke that the reasons EPA gave for firing Marcus were a pretext and “the true reason for the discharge was retaliation.”

Reich wrote that he found particularly disturbing that Marcus’ supervisors accepted the charges against him “in the absence of any convincing documentation.”