The 752-foot Overseas Reymar rammed the tower on Monday afternoon as it headed out to sea, according to the Coast Guard and state transportation officials.
The unidentified pilot will also report to the state Board of Pilot Commissioners, which will conduct its own investigation of the accident. That board regulates bar pilots.
The pilot has been a San Francisco bar pilot since 2005, said Charlie Goodyear, a spokesman for the San Francisco Bar Pilots Association. The association did not release his name.