The ferry system says it happened Saturday at the Eagle Harbor maintenance facility where the ferry was undergoing routine annual maintenance.
Crews had drilled one hole in the bilge deck to drain dirty water and paint chips. They were drilling a second hole nearly 2 inches in diameter when it breached the hull.
Workers made a temporary repair with a clamp on the inside and pressure patch on the outside. A permanent repair planned this week will delay the ferry's return to service.
It isn't the first time that routine maintenance has gone awry on the 44o-foot Walla Walla.
In November 2012 a drive motor was burned out by a mistake during maintenance work. Fixing that mistake cost $3 million and took several months.
Built in 1972, the Walla Walla can carry 188 cars and 2,000 passengers.