The base was partitioned off at certain sectors so it was isolated to one area, Mr Clarke said.
"At this stage we're still waiting for assessment to come back to give us an idea of what actually caused the accident - it looks like we may have hit something first or something like that, but we're not too sure.''
He would not comment further until the assessors had been in touch.
Nobody was injured during yesterday's incident, but police reported some passengers were suffering from sea sickness.
Inspector Ian Booker of police northern communications yesterday said the vessel was an 18 metre power catamaran with a capacity of 60 people. However, the vessel was "nowhere near capacity'' at the time of the incident.
Maritime New Zealand had been advised of the incident.