The former director of special programs at the Department of Agriculture's Graduate School and his wife were indicted yesterday on charges they ran a bogus consulting scheme that defrauded the Army of $53,500.

Lee Scott and Donna Varner of Annapolis were accused of repeatedly billing the Army for $250-a-day consulting work supposedly performed by a Silver Spring woman between March 1983 to August 1984. The 17-count indictment, returned by a federal grand jury in Alexandria, said the work was never performed.

The alleged consultant, Linda O'Brien Hosein, kept 8 percent of the money and gave the remainder, or a total of $49,200, to the Varners, according to the indictment.

Hosein, named as an unindicted co-conspirator in the indictment, pleaded guilty in June to a criminal information charging her with two misdemeanors of fraudulently receiving less than $100 from the Army.

Under an agreement with the prosecutor she was given a two-year suspended sentence, ordered to do 200 hours of community service and pay back the money she received from the Army. She agreed to cooperate with the government in its investigation of the Varners, according to court papers.

Varner joined the USDA Graduate School, which specializes in adult education, in 1969 and became director of special programs in January 1977, according to a spokesman for the school. Varner resigned in April 1984, he said.

At the time of the alleged offenses, the school was running educational centers for the Army.

The Varners, who face a maximum of 90 years in prison and up to $170,000 in fines, could not be reached for comment.