No passengers were injured.
The incident involving the 34m aluminium catamaran Pride of Milford, operated by Southern Discoveries, has been reported to regulator Maritime New Zealand.
Southern Discoveries chief executive Tim Hunter confirmed the collision yesterday.
He said it happened about 12.30 on Monday when the 16-year-old Pride of Milford was coming in to berth at the observatory and its port bow ''clipped the pier'' because of wind gusts coming up the sound.
It was a ''low speed'' collision, with the subsequent damage above the waterline, and Mr Hunter said no passengers were injured.
The 10m deep underwater observatory is part of the Milford Discovery Centre at Harrison Cove in the Piopiotahi marine reserve, also a kayaking area.
It is several kilometres from Milford Sound township.
Pride of Milford, which can carry up to 400 passengers, was recently in Dunedin for a six-week stay for survey, maintenance and upgrade work costing more than $200,000.
Mr Hunter said the vessel would be repaired at Milford over the next few days.
Since it was the low season, other vessels were available to take tourists to the observatory, he said.
A new $1.7 million, 17m aluminium catamaran built in Auckland is due in at Milford Sound today.
It will be used specifically for taking tourists to the floating observatory.
The Lady Sterling is surveyed to carry up to 80 passengers.
It would be in training for the next two weeks before starting its duties, Mr Hunter said.
Pride of Milford works alongside the 100-passenger, 21m monohull Lady Bowen, 240-passenger, 26m catamaran Spirit of Milford and 12-passenger, 15.5m monohull Milford Discovery, a charter vessel.
