Fullers360 Chief Operations Officer Paul Trotman says up to five percent of its 5000 trips a month are being cancelled.
He says the disruptions are disappointing and he apologises to customers for them.
The Auckland ferry operator is desperately hunting for staff as criticism over disrupted services mounts.
A Devonport ferry broke down midway across the Waitematā Harbour earlier this week. Today's cancellations include trips on the Half Moon Bay, Bayswater and Devonport Ferries.
Customers have complained of ferries leaving ahead of schedule, boats too small for the commuter crowd, and last minute cancellations with no reason given.
