If convicted, Sanford could be fined up to US$500,000 per count or twice the gross gain or loss that resulted from the criminal conduct.
The indictment also seeks criminal forfeiture from Sanford of more than NZ$24 million for proceeds derived by Sanford as a result of the criminal conduct.
The case was investigated by the United States Coast Guard and is being prosecuted by the United States Attorney's Office for the District of Columbia and by the Environmental Crimes Section of the Environment and Natural Resources Division of the Department of Justice.
In a statement to the stock exchange, Sanford said it had learned of the indictments today.
"We have been conducting our own investigations in conjunction with our legal advisers since July 2011 when the US detained the San Nikunau in American Samoa. We will be vigorously defending all the charges and continuing our efforts with authorities in American Samoa to get the vessel released to enable it to return to fishing,'' it said.
The company said it took its responsibilities seriously ''and would never permit discharges of pollutants into the ocean and nor would we obstruct any reasonable investigation into any allegations made against the company''.