Two spectators to a secondary school athletics event were seriously injured when a two-tonne metal structure was picked up by a wind gust, thrown over a fence, and landed on them.

The incident happened at the New Zealand Secondary Schools Athletics Association championships in Newtown Park in Wellington shortly before midday on Saturday.

Association President Tony Rogers said the structure that got picked up in the gust was a "very large pole vault cover" on four wheels. It usually need four to six people to move it.

It was estimated to weigh "a couple of tonnes", he said.

But a freak gust of wind - which didn't even disturb nearby tents - lifted it up, over a fence, over a pathway, and onto a steep grass bank where it landed on top of two spectators.

Officials, participants, and others rushed to help, Rogers said.

Wellington Free Ambulance confirmed it took two people from the park to Wellington Hospital with serious injuries after a weather and wind related incident.

The road race championships at the tournament were cancelled due to poor weather.

A Wellington Free spokesperson said another person in Wellington was injured by flying garden furniture on Saturday.

According to MetService, the strongest wind gusts in Wellington were 100kmh in Kelburn, and 96kmh at Wellington Airport.

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