A Washington service station operator was arraigned in federal court here today on interstate theft charges stemming from what the FBI called a massive check-kiting scheme in which more than $29 million in checks were cashed at a Washington bank to cover overdrafts at a Maryland bank.

Eddy Marvin Thompson, 39, of suburban Baltimore, who operates Thompson's Texaco at 4000 Georgia Ave. NW, was released on personal recognizance by U.S. Magistrate Paul M. Rosenberg after pleading not guilty to a 23-count indictment charging him with interstate transportation of stolen money.

FBI spokesman Andrew Manning said the alleged scheme worked this way: Thompson maintained a personal checking account at Citizens Bank & Trust Co. of Maryland in Riverdale and a business checking account at American Security Bank in Washington.

During a six-year period ending in early 1982, Manning said, Thompson wrote checks on his personal account on a daily basis--usually overdrawing the account--and deposited the checks in his business account at American Security to pay his business bills. Next, Manning said, Thompson wrote another check on his personal account in Maryland, cashed it at American Security in Washington and then returned to Maryland to deposit the cash to cover the previous day's overdraft.

At first Thompson allegedly wrote checks for a few hundred dollars but the amounts mushroomed to as much as $200,000 on each check by early 1982 when an investigation by authorities brought the scheme to a halt, Manning said.

With the money constantly moving in and out of the two banks, Manning said, Thompson cashed checks totaling $29,674,334 between February 1979 and December 1981. American Security ultimately lost about $200,000, the amount of the last check Thompson cashed there before the scheme was stopped, Manning said.

Clement T. Cooper, an attorney representing Thompson, acknowledged in a telephone interview that Thompson deposited and cashed numerous checks at the two banks but said Thompson was innocent because he lacked criminal intent.

Cooper faulted American Security for permitting Thompson to cash such large checks indiscriminately, saying the bank failed to file currency transaction reports (CTRs) to the U.S. Treasury Department as required on amounts of more than $10,000.

The purpose of the CTRs is to alert law enforcement agencies to unusually large transactions, officials said. The investigation into the Thompson case began after federal authorities checked CTRs filed by the Citizens Bank in early 1982, sources said.

Cooper said American Security fired a branch manager and two assistants for alleged mismanagement in the Thompson case.

An American Security spokesman said there is "no basis in fact whatsoever" in Cooper's allegations and noted that the bank successfully sued Thompson for recovery of the $200,000 last year. Cooper has appealed that judgment.