A former clerk in the finance office of the Australian Embassy here who stole $671,802 from the embassy and fled to Rio de Janeiro and Greece was sentenced yesterday in U.S. District Court to three years in prison.

Judge Barrington D. Parker also ordered John Ian Cowling, 35, to pay a $10,000 fine and to sign over to the U.S. government $11,000 in travelers checks that were recovered when he was arrested in Greece a year ago.

Under the terms of the sentence, the British-born Cowling, who is wanted in England on a charge of stealing $300,000 from a man who hired him about six years ago as a butler, must serve the full term in prison. Parker said the time Cowling has spent in jail since his arrest could be deducted from the sentence.

Cowling, who worked as a $12,000-a-year clerk in the embassy's accounting section reviewing payment claims and vouchers, pleaded guilty in November to diverting the money to a dummy bank account and then fleeing the country. He had maintained that he took the money to show embassy officials there was a flaw in the financial system they used.

Parker said yesterday that Cowling's explanation was a "story that won't fly."

Cowling forged the names of two embassy officials on a voucher and had a $671,802 check sent to a dummy account at a Riggs National Bank branch here instead of to the company in Florida that should have received the funds. The scheme was discovered when the company inquired about the money.

By then, Cowling had withdrawn $61,000 in cash and the rest in a cashier's check, which he deposited in a bank in Brazil. He got $183,000 in traveler's checks from that account before U.S. officials notified the bank to stop payment.

Cowling fled to Rhodes, Greece, after learning of the stop-payment order, and opened a discotheque there shortly before he was arrested.