Although the Superflyte was initially hit by a piston problem, the company last night said it had discovered "some other issues" likely to take another week to 10 days to repair.
"It's about making sure that while we've got it off, we fix it properly, so when she comes back, she comes back in a reliable way," said Fullers operations general manager Tim Palmer.
He confirmed that would-be passengers on yesterday's 8am sailing from Waiheke to Auckland had to wait for the following 9am service after the Starflyte reached its capacity of 306 people.
A woman who starting queuing early enough to get a seat told the Herald a party of school children squeezed on to the vessel ahead of regular commuters.
Mr Palmer said the company had been aware of the school outing, but had planned for the Superflyte to be back in service yesterday.
Although the problem is most acute on the Waiheke run, Devonport passengers are also having to cram on to what one called "a motley assortment" of vessels while the Kea, their regular ferry, is out for extended maintenance.
Auckland Council's member for the Waitemata and Gulf ward, Mike Lee, said Fullers generally operated a very good service - "I would say the best public transport service of all the operators" - but was letting itself and its passengers down with the age of its ferries.
"They are old, worn out," he said.
"The fact is, their owner in Scotland [Sir Brian Souter] is taking money out rather than putting it in.
"Auckland Council and Auckland Transport should not be worried about fluffing about changing the ferry terminals at great expense. We need to focus on the real problem that our ferries are becoming increasingly aged."
Mr Palmer said the company was about to receive its second new ferry this year, the 334-seat Te Kotuku built in Wanganui for about $8 million for delivery next week, and was upgrading the Kea and the Adventurer.
Waiheke fleet hit
Quickcat: Suffered hull and propeller damage two weeks ago from storm debris - due back early October.
Superflyte: Hit by mechanical problems this week - not due back for up to 10 days.
Kea: Under planned maintenance including installation of a new control system - expected back late October
Adventurer - under planned maintenance including installation of a new control system - almost ready for service.