Tuesday's service departed Wellington at 9am and was due to arrive in Picton at 12.30pm - but was only able to finally berth at 9pm.
Passengers on the smaller Bluebridge ferry were in for an even longer haul, with their ferry having departed the capital at 8am.
Interislander general manager Walter Rushbrook said the afternoon had been a one-off event.
"We've got people who have been on our team for four decades and they can't recall ever having a circumstance like this before the wind is so strong we haven't been able to berth for a while.
"It's not uncommon to maybe have a brief gust of wind which means we maybe have to abandon berthing for a few minutes and do a second attempt, but having to spend all afternoon and part of an evening not being able to berth is highly unusual."
He said the Interislander was back on timetable on Wednesday, with the 9am Kaitaki service to depart as scheduled.
There was a slight backlog of services due to the disruption on Tuesday, but that would be cleared within 24 hours.
Rushbrook said there had been no indication there would be a delay when Kaitaki departed Wellington yesterday.
"Around about lunchtime Kaitaki was coming into berth to Picton and during the manoeuvre there was some big, big wind gusts, over 140km/h.
"A decision was made by the crew on board to abandon the manoeuvre and they moved back out into the Sounds."
At one point passengers had been concerned they may have to return to Wellington, but everyone was in surprisingly good spirits, he said.
"It was frustrating but no one really seemed to be getting too upset.
"Even though it was very windy it wasn't actually too rough in the Sounds, so people weren't being sick everywhere.
"I was actually surprised at how good the mood was to be honest."
Crew had provided regular updates as well as tea and coffee for passengers, he said. One staff member had been completing her very last voyage, which ended up being eight hours longer than anticipated.
"They apologised, they said the wind had turned out far, far stronger than they had expected," Rutherford said.
The Interislander vessel eventually berthed in Picton just after 9pm.
"There was no drama at all pulling in to berth, it was almost like classic textbook berthing."
