The inspector general of the Department of Health, Education and Welfare charged yesterday that Food and Drug Administration officials used $50,000 of federal funds to shore up the shaky finances of a Maryland nutrition society.

A three-year audit and investigation of an FDA grant to the Nutrition Today Society concludes that while the society received $49,800 to supply teaching aids, such as film strips, to the FDA, only the $1,102 worth were delivered.

The report of the inspector general alleges that there were "serious irregularities in awarding the grant - a process in which the then FDA Commissioner Alexander Schmidt directly participated." It also says that prior to its approval, the grant application was reworked by FDA officials, "one of whom was also on the board of the Nutrition Today Society."

HEW Inspector General Thomas D. Morris said in the report the teaching aids to be delivered under the December 1975 grant had already been produced and advertised by the Anapolis-based society at prices far below those charged to FDA.

In any case, the report said, there was no planned use for the teaching aids by the FDA, and some of them went into storage, where they have never been used.

The funds from the grant, according to the report, were transferred from the society to its profit-making - and therefore ineligible - affiliate Nutrition Today Inc., for general operating expenses.

Dr. Cortez F. Enloe Jr., editor and publisher of the Nutrition Today magazine and executive vice president of the society, is out of the country and could not be reached for comment.

The society's lawyer, F. Trowbridge vom Baur, said that he has supplied the inspector general with a detailed rebuttal of the report's findings, which vom Baur characterized as "grossly and uttlerly erroneous."

Schmidt, now vice chancellor for health services at the University of Illinois, said yesterday that he does not believe any irregularity existed in awarding the grant, though he did know the society was having some limited financial problems and was personally acquainted with Enloe.

"I thought that the teaching aids were excellent," said Schmidt, who added that he still subscribes to the magazine.

Morris said that every effort is being made to recover the funds. When the matter was first brought to light in 1976, the Justice Department declined to prosecute Enloe on fraud charges. But Morris said that Justice has since advised him it is re-evaluating the possibility of prosecutions under federal conflict-interest statutes.