The Hong Kong-based operator of a container ship that struck a bridge support in the San Francisco Bay last year has been indicted for allegedly doctoring paperwork in an attempt to thwart the investigation.

A federal grand jury charged Fleet Management Ltd. on Tuesday with six felony counts of making false statements and obstructing justice. Prosecutors announced the indictment on Wednesday.

Unidentified "senior ship officers and shore-based supervisory officials concealed and covered up documents with an intent to impede, obstruct and influence the investigation of the spill," according to a Department of Justice summary of the indictment.

Among the allegedly falsified documents were the ship's passage plan for its scheduled Nov. 7 journey from the Port of Oakland to South Korea, and for two trips a few days before the crash.

Under U.S. law, passage plans are required for each voyage. Fleet Management "falsified and forged these plans after the crash and concealed and covered up the real ship records," prosecutors said.

The indictment also charges Fleet Management with two counts of misdemeanor crimes under the Clean Water Act and the Migratory Bird Treaty Act for negligently causing the crash, which dumped 53,000 gallons of toxic bunker fuel into the bay. The spill killed and injured thousands of birds and fouled beaches throughout Northern California.

The negligence allegedly stemmed from Fleet Management's failure to adequately train a new crew it had installed after taking over operation of the Cosco Busan and for failing to post an adequate lookout.

Under the latest environmental crimes indictment, Fleet Management is charged as a co-defendant alongside Capt. John Cota, the ship pilot whose job was to guide the giant container vessel from the port out to sea.

Cota has been charged with two felony counts of lying to Coast Guard officials about his prescription drug use and two misdemeanor environmental crimes.

Fleet Management could face fines of $500,000, or twice the losses caused by the alleged violations, for each obstruction and false statements count. The penalties for the Clean Water Act violations could range as high as $200,000, or twice the losses. The migratory bird count could bring fines as large as $10,000 or twice the losses.

Fleet Management is already being sued by the Justice Department for allegedly breaking environmental laws. The lawsuit filed last year accused Fleet Management and others of "fault, negligence and breach of federal safety and operating regulations."

Fleet Management said in a statement Wednesday that it had discovered that "discrepancies exist between the facts as understood and reported prior to its investigation." It did not elaborate, but said it had advised the Justice Department of its finding and "suspended the individuals involved in the misunderstanding of the facts."

The company said, though, that it "does not believe that these new facts have any bearing on the accident or on the pilot's navigation of the ship."

The ship's owner, Regal Stone Ltd., which hired Fleet Management, said it "noted with disappointment" the new indictment.

The new charges of falsifying documents come as prosecutors are investigating the possibility that the ship's Chinese crew altered certain unidentified records after the crash. It was not immediately clear whether the indictments and that thread of the probe are connected.

Josh Eaton, a spokesman for U.S. Attorney Joseph P. Russoniello, declined to comment on anything beyond what was in the indictment.

Jeff Bornstein, an attorney for Cota, said he reviewed evidence from prosecutors that showed crew members had admitted in the last two months they had not been adequately trained and had falsified "key navigational records." The doctoring of certain documents, including passage plans, had been done "at the direction of a very high-level Fleet official in the hours or days after the accident," Bornstein said.

The new charges bolster Cota's contention that "this was a series of errors that involved other people and other factors," Bornstein said in a telephone interview.