Sanford was sentenced in a US Federal Court in Washington following a two week trial in August last year.
The court ordered that a further Community Service Payment of $US500, 000 be paid to the US National Fisheries Foundation.
Sanford has been sentenced to three years probation, during which time it is banned from entering US ports until approved audits of the Company's Environmental Compliance Plan have been completed. The first audit is scheduled in February.
Sanford's lawyers argued at the hearing that the US Justice Department's call for the maximum US$3 million fine and a five year probation period, including a ban on Sanford boats entering US waters, was "excessive", local media reported.
Managing director Eric Barratt says the company accepts the judgement, and just wants to get on with running its business.
Criminal charges were filed against Sanford in January 2012 alleging the crew of Sanford's biggest tuna boat, San Nikunau, repeatedly illegally dumped bilge water contaminated with oil into the ocean near American Samoa, and then tried to cover it up.
The oil was never spotted, but US authorities discovered falsified records on board.
The US jury convicted the company of six of the seven charges it faced.
It's not the first time Sanford has been convicted of discharging contaminants - it has two previous convictions, the most recent in 2006.
San Nikunau's former chief engineer, James Pogue, was today sentenced to one month in prison, five months home detention and 18 months probation for falsifying records.
