The problems have left riders grumbling about long waits and cancellations during the peak summer tourism and travel season.
Two vessels required unplanned work at the same time two other ferries were out for scheduled maintenance, Capt. George Capacci said.
"It's an unprecedented situation we find ourselves in," Capacci told reporters in a conference call.
He apologized to riders and said the ferry system is fragile and vulnerable to disruptions due to an aging fleet and deferred maintenance.
Service has been troubled since Tuesday, when the ferry Tacoma lost power on the busy Seattle-Bainbridge Island route and a ferry was shifted from the Edmonds-Kingston route, causing delays for those riders.
No estimate was available for the return of the Tacoma, which has an electrical problem, Capacci said.
Service should return to normal this weekend with the return of the Wenatchee, which has been in dry dock in Vancouver, British Columbia, to repair a leak.
As part of the shuffle, service was canceled Thursday and Friday on the run between Anacortes and Sidney, British Columbia. That boat was sent to restore two-boat service on the Edmonds-Kingston run.
The system had little flexibility because the Yakima is out for motor maintenance and the Kitsap for painting, Capacci said.
Washington State Ferries operates 22 vessels - the largest such fleet in the U.S. - on 10 routes across Puget Sound. State ferries carry more than 23 million commuters, tourists and business passengers a year.
The state is in the process of adding three Olympic-class ferries. The Tokitae (toh-kee-tay) is in service. Another vessel is under construction and one is planned.
The state Transportation Department also is in the process of finding a permanent ferry system director to replace David Moseley who resigned in April.