Troubled Interislander ferry Aratere was damaged berthing into Wellington Harbour about 3.30pm on Thursday, Wellington's harbourmaster confirmed to RNZ.
There is a hole in the hull but it is high on the ship, and no injuries are reported.
KiwiRail said in a statement that while docking in strong winds, the ferry made contact with the link span, the dock ramp which allowed vehicles to access the vessel.
Interislander said the damage was minor, but repairs on the ferry and the link span would continue overnight.
"Aratere made low-speed contact with the link span - the dock ramp that allows rail to access the vessel," executive general manager Duncan Roy said in a statement.
"As a result, there was some damage to the link span, and to the hull of the vessel well above the waterline."
There were 106 passengers and 40 crew on board, KiwiRail said.
A passenger on the ship told RNZ there seemed to be a problem berthing this afternoon.
They said passengers were being fed hot chips, tea and coffee and were now being allowed to leave the ferry.
Just after the confirmation of the damage, they said cars were disembarking.
The 4.30pm sailing from Wellington was cancelled and passengers were asked to wait for the 8.30pm sailing.
"We anticipate Aratere returning to service over the weekend. Affected passengers are being transferred to alternative sailings," Roy said.
The Interislander ferry ran aground on 21 June just north of Picton while on a freight-only sailing.
It only returned to passenger service at the end of July.
Interislander's three ferries were all built in the 1990s and have been hit by mechanical problems in recent years and there has been increased debate about replacing the ships.
In July, ship assessors found the ferries were in better shape than previously thought, and would be fine to sail for five more years.
A similar accident tore a hole in the hull of another Interislander ferry, the Kaiarahi, in November last year.
The government has been criticised for pulling funding to the iReX project, with the maritime union warning the cancellation cost could reach half a billion dollars.