(04-09) 04:00 PDT Washington - --

The pilot of the container ship that sideswiped the Bay Bridge and spilled 53,000 gallons of fuel oil into the bay was convicted of drunken driving in 1999 and was taking medication for depression, anxiety and sleep apnea that could have impaired his ability to steer the ship, federal officials said Wednesday.

National Transportation Safety Board investigators also grilled Coast Guard officials about why they approved Capt. John Cota's license last year after he presented the agency with the list of drugs he was taking.

"I wouldn't want anyone taking those medications and having to make decisions in safety-sensitive positions," testified Dr. Robert Bourgeois, who evaluates mariners for the Coast Guard and airline pilots for the Federal Aviation Administration.

NTSB investigators also unearthed new evidence of an Oct. 9, 2004, incident in which Cota became enraged at the crew of the Navy amphibious assault ship Tarawa, which he had boarded during Fleet Week.

Cota demanded that the crew remove "tag lines," which are used by the crew to hoist the pilot ladder but can be dangerous for bar pilots when they board. When the crew refused, he pulled out a pocket knife and cut them off. The captain and crew said he used offensive and derogatory language during the whole encounter.

After the incident, Cota was pulled from regular duty for five months, and a review panel concluded that his conduct was unprofessional and "had the potential of distracting the bridge team from the safe navigation of the vessel."

Safety board chairman Mark Rosenker appeared stunned that the San Francisco Board of Pilot Commissioners, a state agency, allowed Cota to remain an active pilot despite his having at least four major safety incidents - including the grounding of a freighter in 2006 - as well as the Tarawa episode.

"How many strikes does it take before you are out of the game?" he asked.

The revelations were another blow to Cota, who is facing criminal charges in the incident involving the freighter Cosco Busan. The 27-year veteran pilot refused to testify before the board because of his pending trial.

But his attorney, Jeff Bornstein, said there is no link between Cota's prescription drug use and the accident on Nov. 7. Bornstein said it was unfair to dredge up Cota's decade-old DUI conviction without noting that he tested negative for drug and alcohol use on the morning of the crash.

Cota was taking several drugs

"The way information is coming out is making it impossible for him to get a fair trial," Bornstein said. "How could people not have made up their minds based on what the government is saying?"

The revelations came on the last of two days of hearings in Washington by the safety board, which is charged with determining what caused the accident and ensuing oil spill. Rosenker said his agency will release a draft of its accident report this fall.

NTSB investigators are clearly focusing on Cota's past and present behavior.

Cota was arrested for driving under the influence in February 1999 and immediately went into alcohol treatment at a rehab center, federal officials said. His most recent medical report indicated that he suffered from pancreatitis, a condition often linked to alcoholism.

According to a medical report prepared by his doctor, Cota was taking Wellbutrin, a drug to combat depression, as well as medication for migraines and glaucoma. He also suffers from sleep apnea, a condition that makes it hard to get into a deep sleep and often leads to drowsiness. At night he uses a CPAP - a breathing machine that pumps air to keep his airways open - and during the day he takes Provigil, a drug that can help fight drowsiness.

Cota's medical records show he was also taking Lorazepam, an anti-anxiety drug. Bourgeois said the FAA will not allow its pilots to take the medication because it can stay in their system and have effects for as long as 12 hours after it has been ingested.

"That is not something you would want to have on board," he said.

Bourgeois was asked whether he would allow his children to ride a school bus operated by a driver who took the same medications. "They wouldn't get on the bus," he replied.

Coast Guard officials acknowledged that they did a poor job of reviewing Cota's medical files. In documents released late Tuesday, George Buffleben, the chief of the Coast Guard's San Francisco Regional Examination Center, told investigators that at the time he believed a doctor's certification that Cota was fit to continue his duties.

Coast Guard Capt. Arthur French, a doctor who oversees the agency's medical review team, acknowledged Wednesday that there are some holes in the Coast Guard's system of reviewing health records. He said new rules now in effect would have flagged Cota's medical file for further review because of his sleep apnea and the medication he was taking.

"We would want to see evaluations from the specialists," French said.

Involved in 12 incidents

NTSB officials released a list of 12 incidents in which ships were damaged and Cota was involved, although not all of the incidents were caused by pilot error. Mike Miller, the president of the San Francisco pilot commissioners board, which oversees bar pilots, insisted that Cota had a 99.7 percent error-free record.

"He had more incidents than others, but only by a tiny number," Miller said.

But other NTSB officials suggested that Miller, an appointee of Gov. Arnold Schwarzenegger, and his board should have taken more aggressive action after Cota was involved in several major incidents in the last decade.

"If you look at Capt. Cota's record, there certainly appears to be a pattern," said Dr. Barry Strauch, one of the NTSB's lead investigators. "Why did the commission miss the pattern of performance degradation that we see in Capt. Cota's performance, particularly over the last 10 to 12 years of his career?"

E-mail Zachary Coile at zcoile@sfchronicle.com.