Fairfax County authorities yesterday directed three youth sports groups to "cease all bingo operations immediately" at a parlor run by a man who is under investigation by police for running allegedly illegal bingo games.

The County's order said the organizations, which used their share of bingo profits to support sports teams, violated state and county laws by contracting with United Charities Inc., an Alexandria corporation controlled by Alva Ford Thompson, to run their bingo games.

The two-year-old Virginia law requires that charities run their own games using volunteer workers, requirements that area prosecutors say prohibit "middle men" like United Charities from operating the games.

Separately , an Alexandria Circuit Court judge upheld the validity of a search warrant issued last Friday that resulted in the seizure by police of thousands of bingo-related items from Thompson's Alexandria office.

Thompson, who has not been charged with violating any bingo law, was named in an affidavit filed last week by a police undercover agent. The affidavit, by officer Kathleen Bra-love, accused Thompson with skimming profits and falsifying financial data to "mislead and defraud" Alexandria authorities and the charitable organizations whose games he operated.

In letters sent to the three Fairfax County organizations, Gilbert R. Knowlton, director of county zoning enforcement, warned them that failure to stop the games would "constitute a misdemeanor punishable by a fine of up to $1,000."

Only one of the three organizations - the Mount Vernon Youth Association - had a county bingo permit last year, Knowlton said.

Commonwealth's Attorney Robert F. Horan, the county's chief prosecutor, said yesterday he is investigating why the other two groups, "Pioneer League Baseball" and "Lee District Basketball," failed to have a permit.

Knowlton said yesterday the contracting arrangement between the athletic organizations and United Charities was uncovered in an audit of records submitted by the groups for a 1978 bingo permit.

The audit prompted Horan to request a police investigation of the bingo operation last week. "The audit indicates there is a possibility of a violation," Horan said yesterday, "but it is not clear who is responsible."

Horan said he met last week with county police detectives to direct them in an investigation of "who or what is involved." He said he did not know whether the Fairfax investigation would overlap with the one now being conducted in Alexandria.

The Fairfax bingo operation was located at Bonanza Bingo hall at 7520 Richmond Highway south of Alexandria. The audit of the groups' records shows that Thompson leases the hall and runs bingo games there, Knowlton said.

Treasurers of two of the athletic organizations involved said yesterday they were "not surprised" by the county action because of what they have heard about other investigations of Thompson in Alexandria.

"It seemed a logical progression that if this is going on in Alexandria, the same thing may be going on around here," said Clarence L. Moore, treasurer of the Mount Vernon Youth Association.

Moore said that United Charities has been conducting bingo on behalf of his organization since April, 1977, and the profits turned over since then to the youth association have totaled about $8,500. The money, Moore said, has been accounted for and has been spent on sports equipment. "The loss of [bingo] funds will definitely hurt the organization," Moore said.

Moore said some members of his organizations have complained about what they said was a sharp difference between profits made by United Charities and profits turned over to the athletic association. "But no one in our organization had ever been involved in bingo of any magnitude and we didn't know what kind of profits to expect."

Robert V. Farabaugh, treasurer of Pioneer League Baseball, said the loss of revenue from the bingo operation, which earned about $5,000 for the group since last July, will hurt us obviously."

Farabaugh said his organization applied to the county last year for its own bingo permit, but got no response and decided to contract with United Charities while it waited for a permit. United Charities did not have a bingo permit last year, Knowlton said.

The letter Knowlton sent the organizations also mentions a "lack of control over gross receipts'''' from bingo and says "it cannot be certified that the proceeds have been spent for legitimate expenses or charitable purposes."

Both treasurers said they know of no irregularities in their organizations records.

County spokesman Edmund L. Castillo said yesterday there are about 90 nonprofit organizations, mostly churches, with bingo permits in Fairfax. The revocation of the bingo permit yesterday was the first such action ever taken by the county, Castillo said.