The FBI and Virginia officials are investigating allegations that a former small town banker who has acknowledged taking $360,000 from his bank may have taken $29,000 from the town's treasury as well.

Officials in the town of Remington said yesterday that the probe is focusing on allegations that William E. Embrey took almost one-fourth of the town's budget during the past two years.

Embrey, 38, was removed as president of the State Bank of Remington on Aug. 25 after he acknowledged using bank funds to finance various real estate ventures in the Fauquier County area, 50 miles west of Washington. He later resigned as treasurer of the town of 350 after details of his ouster from the bank became public.

Town Council member James Meadows said the investigation began when FBI agents probing the bank's troubles presented officials with "three or four checks" made payable to Embrey and endorsed by him as town treasurer. "When we saw those checks everybody could have gone through the floor," Meadows said.

Embrey, who had previously denied taking funds from any source other than the bank, declined to comment yesterday on the town investigation. Town officials said that the former banker had deposited $30,000 in an escrow account when their investigation began six weeks ago. That amount should "reasonably be expected" to cover all the losses, Mayor W. Wynant Hoffman said.

Charles Monroe, special agent in charge of the FBI'S Alexandria office, said the bureau gave some "questionable checks" to the town officials and that the agency also is investigating town accounts because federal revenue-sharing funds are involved.

Town officials said they are at a loss to explain how almost a quarter of the town's budget could have been taken without their notice. Including sewer and water accounts, Remington's annual budget totals about $60,000.

"As far as we knew our town accounts were correct," said Mayor Hoffman. "We didn't have any creditors coming to us saying we owed them money."

Hoffman said that no criminal charges would be filed until a full audit report is made to the council. The town's books are being audited back through 1977, he said.

FBI officials said their investigation into the town and bank accounts would be completed "within 30 days."

Embrey has engaged the Washington law firm of Williams and Connolly to represent him during the investigation. As town treasurer he was the only paid Remington official and was entitled to 5 percent of the budget or about $3,000 annually. The $29,000 in improper checks, drawn in amounts of $4,000 or $5,000 each, did not represent Embrey's salary, according to Meadows.

Meadows said that town officials had assumed that road and sewer repair work were eating up town funds. Embrey had reported small surpluses of "less than $5,000" for the town for the last several years, town officials said.

Townsfolk were astonished when Embrey, regarded as one of the town's leading citizens, was ousted from the bank and later resigned as town treasurer and chairman of the Fauquier County Democratic Party.

In a newspaper interview earlier this month, Embrey did not dispute allegations about his use of bank funds. "I'm sure it's some kind of embezzlement or fraud of some kind," he said. "I don't think there is any question I'm guilty."

Mayor Hoffman said yesterday he had known "Embrey all my life and everywhere you turn people only had good to say of him. If you ask why nobody looked into these things earlier, that's your answer right there."