Former Fairfax City treasurer Frances L. Cox has been indicted on a felony embezzlement charge after a month-long investigation of alleged financial discrepancies in her office between August 1979 and last December.

The indictment, made public yesterday, gave no details on how much money allegedly is missing from city accounts. City officials said, however, they have been unable to account for about $150,000. Cox's successor quit earlier this year after three weeks on the job, saying he was unable to straighten out the city's tangled finances.

The funds in question represent revenues from "taxes, dog tags, city stickers, water bills--you name it," said city spokesman Thomas Welle.

Cox, who left her elected position in January after 27 years in the post, pleaded innocent yesterday during a brief arraignment and was freed on personal bond. She faces trial Sept. 13 in Fairfax County Circuit Court.

"We feel the indictment has no merit. We've felt so all along," Cox's lawyer, John H. Rust Jr., said yesterday. "I don't think they prosecutors have all the information."

Fairfax County deputy prosecutor Steven Merril said the Fairfax City Council requested the investigation a month ago after they were alerted to a "possible criminal operation" in the treasurer's office. Merril said the investigation revealed an alleged "common scheme of embezzlement," but declined to give specifics.

The investigation is continuing, Merril said, with Cox as its only focus.

Cox was unseated in last fall's election by Ray M. Birch. Birch resigned shortly after taking office, saying he had found cash stuffed in desk drawers, checks left unrecorded, and $1.5 million in discrepancies between bank deposits and treasurer's reports. Birch also said he was notified by a bank the city's account was $156,000 overdrawn.

The council named John W. Coughlan to fill the vacant position until this November, when a new treasurer will be elected. There is expected to be at least a five-way race for the $35,000-a-year post.

If convicted, Cox faces a maximum penalty of 20 years in prison and a $1,000 fine.