Karl S. Bowers, former federal highway administrator, will be arraigned Thursday in Charleston on charges of conspiracy, fraud and embezzlement.

Bowers, 36, who resigned his post in the Department of Transportation in January, was indicted last week by a federal grand jury with two others. They were charged with conspiring illegally to buy and sell seven federally financed houses in Hampton County, S. C. Bowers alone is charged in a 15-count indictment with conspiring to defraud the United States and submit false claims to the Department of Agriculture.

A five-count indictment charges Bowers; his younger brother, Lee Bowers, and Henry F. Glover Jr., former Hampton County supervisor for the Farmers Home Administration with conspiracy to defraud the United States and misapplication of FHA monies. FHA is a division of the Department of Agriculture.

Bowers said today, he is innocent and intends "to fight this with all resources available." Bowers learned of the indictment on the news but said he was aware of the seven-month-long investigation because his brother was interviewed. He added, "But nobody contacted me. I thought surely if they felt the charges had any substance at least they would have approached me."

The charges against Bowers include five counts of receiving improper payments while employed as a federal official, an alleged violation of federal conflict of interest laws. Bowers served as federal highway administrator from May 1978 until last January. The 15-count indictment covers the period from Dec. 1, 1975, to May 31, 1979. The five-count indictment of his brother and Glover, covers from June 1974 to July 1978.

Conviction on a conspiracy charge carries a maximum penalty of five years imprisonment and a fine of $10,000 or both.

Bowers served from 1973 to 1977 on the South Carolina Highway Commission. During that time he also operated a real estate business in Estill, S.C. He was a Hampton county magistrate for six years and at one time was president of the state's magistrate association.

Bowers left his federal post, where he supervised 4,000 employes, to become a major in the South Carolina National Guard. He is special assistant to Adjutant Gen. T. Eston Marchant, head of the guard. Marchant said there are no regulations requiring that Bowers be suspended while the charges are pending.

"I have been advised there is no relationship between the matters alleged in the indictments and the duties of his present position. I would assume that like any other citizen he is presumed innocent until proved guilty," Marchant said.