In an eerie echo of half a century ago, bad weather has affected services remembering the sinking of the Wahine ferry in Wellington harbour in which 53 lives were lost.

Tuesday marked the 50th anniversary since the ferry ran aground on Barrett Reef in 1968 in a tragedy that shocked the nation.

But a dawn service held at Muritai School in Eastbourne on Tuesday morning was forced indoors as strong winds and heavy rain lashed Wellington.

Many of the survivors in 1968 were brought to Eastbourne to receive shelter and food and on Tuesday about 500 people, including survivors and some of those who were there 50 years ago, gathered again at the school.

As part of the anniversary, the Interislander ferry Aratere sailed past the Eastbourne service sounding its horn at 6.41am and a wreath was thrown from the deck.

A fleet of around 40 ships will also sail around Wellington Harbour at midday, including some of the vessels involved in the 1968 rescue.

Prime Minister Jacinda Ardern says the day was an opportunity to recognise the "extraordinary" rescue efforts and acknowledge how the disaster affected so many.

"It's extraordinary to me how many lives it continues to touch and that's the nature of these scale of events in New Zealand.

"I was having a conversation with my mother last night who recalls someone from her school being involved (and) my partner's father was on the sailing that followed the Wahine - it runs deep."

Ms Ardern will also shortly talk at a commemoration service that was previously set to be held at Frank Kitts Park but has now been rescheduled for Shed 6 due to the bad weather.

Kiwirail is supporting commemoration efforts and chief executive Peter Reidy says the Interislander ferry, Aramoana, was also heavily involved in rescue missions 50 years ago.

"KiwiRail and Interislander wanted to help commemorate this event as it's important to recognise the lives that were lost and saved, the brave rescuers involved and the impact it has had on the maritime industry," he said.

According to Maritime NZ, lessons from the sinking of the Wahine led to a positive change in maritime shipping standards.

"Ships in New Zealand, including our Cook Strait ferries, coastal traders and the many overseas ships that visit our country are all safer, in part, because of what happened to the Wahine," Maritime NZ acting director Stephanie Winson said.