Passengers are brought ashore from the stricken East by West Ferry off Seatoun, Wellington.

Passengers say there was pandemonium when a big wave shattered windows and swamped the East by West Ferry in Wellington Harbour, sparking a rescue operation.

Forty-four people, including two crew, were on the 8.05am Dominion Post ferry from Days Bay to Seatoun yesterday when it was struck by what is believed to be a rogue wave as it rounded Scorching Bay.

"It was pretty scary – we went under and all the glass smashed," one of 28 Scots College pupils on board said.

Among them was a year nine boy from St Andrew's College in Christchurch, who has been staying with his grandfather in Eastbourne since last week's earthquake.

Sam Martel told One News he had refused to take off his prized St Andrew's College blazer when told to do so by ferry staff. "I sort of said, nah, I'd prefer to keep my blazer on, because I want to wear it with pride."

Sergeant Scott Miller said it was believed up to 4000 litres of water swamped the ferry when it went nose first into a trough and was swamped by a wave.

A second wave followed, blowing out the ferry's doors. One passenger was washed overboard, but was quickly picked up by the police launch, he said.

That man, and the captain, were taken to hospital, where they were treated for hypothermia. The captain also had stitches for a cut to the head. Both were discharged yesterday afternoon.

Afterwards, the wet but mostly cheerful passengers described the panic on board when the wave hit.

"It was a sinking moment of absolute panic when water came in. It felt like [we were] potentially going to go straight to the bottom ... It was horrendous," David Woodnorth said.

Scots College pupil Carlos Speirs, 13, said it was just pandemonium. He was among pupils on the boat's top level. "I could see the big wave coming then I heard a shattering and a bang. Me and my classmates ran to the back because the ship was at about a 60 degree angle going headfirst into the water."

Commuter Robin Newton praised the handling of the situation by emergency staff. "It was very speedy. People were starting to be off-loaded into the zodiacs [boats] within 20 to 25 minutes."

Among the first on the scene were members of the Worser Bay Surf Life Saving Club, who helped shuttle people to shore, where they were taken to the club before being collected by family.

Many passengers praised the teenagers on board, saying the older pupils took charge and looked after the younger boys.

Anne Manchester said one pupil asked her if she could swim, and offered to help her to shore. "He was the calmest person."

Scots College headmaster Graeme Yule had already received praise for the pupils, and said he was proud of the way they had behaved. The pupils were taken back to the school and given a hot drink and biscuits while they waited for their parents to arrive.

Ms Manchester questioned whether the ferry should have sailed. "It was extremely rough and all of us had felt probably that sailing shouldn't have happened."

Maritime New Zealand is investigating.

East by West Ferries managing director Jeremy Ward said the company would also investigate, but ferries had sailed in worse weather, and it appeared to have been a freak wave.

Water was pumped off the ferry and it was moored at Scorching Bay until the weather calmed enough for it to return to its berth.

The ferry service will operate on a limited timetable until the boat is repaired.

Stormy weather whipped through Wellington yesterday, with gales topping 50 knots (92kmh) in some places.

MetService chief forecaster Peter Kreft said winds were 25 to 30 knots for most of the morning, with regular gusts above 40 knots.