SAN FRANCISCO — The pilot of the container ship that spilled 53,000 gallons of oil into San Francisco Bay was charged yesterday with two felony counts of lying to Coast Guard officials about his prescription drug use.

Captain John Cota, 60, previously was charged with two misdemeanor environmental crimes for his role in the November 7 accident that fouled the bay, killed or injured thousands of birds, and forced the closure of Bay Area beaches.

The new, more serious charges accuse Mr. Cota of lying on annual medical reports in 2006 and 2007 that are required by the U.S. Coast Guard.

The indictment alleges that Mr. Cota “knew that the information he provided was neither complete nor true, including the information … regarding current medications, the dosage, possible side effects and medical conditions for which the medications were taken,” according to the U.S. Attorney’s office.

The indictment, which includes the two previous charges, didn’t provide details about the drugs Mr. Cota allegedly lied about or neglected to include on the two annual medical reports.

The shipping fuel leaked into bay after the Cosco Busan freighter hit a support tower of the San Francisco-Oakland Bay Bridge.