Motorists traveling the Clinton-to-Mukilteo ferry route found themselves waiting more than two hours for sailings throughout the week due to a multi-vessel shuffle in the state ferry system.

The state Department of Transportation, Ferries Division announced in a travel alert Friday that the route’s standard level of service should be restored by this weekend and apologized for the disruption.

“Washington State Ferries apologizes for the frustrating commute you have experienced this week,” the alert said. “We hear your concerns, and we appreciate your patience and understanding as a number of unforeseen challenges have made operating our ferry system especially difficult.”

Ian Sterling, a spokesman for the agency, also called The Record to explain the series of hurdles that resulted in the problem.

“The last week has been a mess,” he said.

State ferries was down a boat last week, the Yakima from the San Juan Islands, for a maintenance issue but unexpectedly lost another boat on Monday, the Jumbo Mark II-class Wenatchee on the Bainbridge-to-Seattle route, due to a bent propeller. It’s believed to have been damaged after striking logs from last week’s storms.

Ferries had to shuffle around a handful of vessels to fill the gaps. To address the loss of the Yakima, the agency moved the Kitsap from the Fauntleroy/Vashon/Southworth route and backfilled that route with the slower Tillikum, a boat already struggling to keep its schedule. The Wenatchee was replaced by the 124-car Kittitas on the Clinton route, which was replaced with the 64-car Kennewick.

The agency reported wait times in Clinton of 90 minutes consistently throughout the week, though residents complained that they were often waiting two hours or more.

“I’m sure people are not real happy, and I don’t blame them,” Sterling said.

The Kennewick was “too slow” to serve the Bainbridge-to-Seattle route, which would have forced missed sailings. Also, the boat lacks the passenger capacity to handle the run’s regular foot traffic; Jumbo Mark II ferries can take 2,499 people and the route operates at near capacity, Sterling said. The Kennewick can take just 748 passengers.

“WSF realizes that this isn’t comforting as you sit in your car for hours waiting to get to work or home, but it’s the factual reasoning behind our decision on boat moves,” Friday’s ferry alert said. “WSF has tried to provide as much service as possible to as many passengers as possible, which admittedly hasn’t had the best result for Whidbey Island residents.”

The agency hopes to have another Issaquah class boat (the same size as the Kittitas) back on the Clinton route by this weekend.