A wild storm system moving across New Zealand on Thursday is bringing swirling winds, surging waves and heavy rains to the capital Wellington and causing flooding in Christchurch.

New Zealand's Metservice announced a severe weather warning for Wellington and nearby regions, with winds of 130 km per hour (80 miles per hour) and waves of seven metres (23 feet) pounding the area.

The weather has caused most flights into Wellington to be cancelled and the ferry services that connect the country's two main islands to be suspended. Waves breaking onto some roads has forced them to close and one of the city's beach suburbs has been cut off.

The National Institute of Water and Atmospheric Research (NIWA) said wind gusts had reached 158 kph at Baring Point, a headland at the southern end of New Zealand’s North Island near Wellington.

Samuel Walsh, who farms in the Wairarapa region in the lower North Island, told 1News that the weather forced him to bring calves in out of the storm and rescue animals that were swimming in his flooded fields.

Radio New Zealand was reporting long queues at Wellington Airport as people waited to see whether any flights would take off this afternoon. The airport said in a tweet that part of the problem was that high winds were making it unsafe for baggage handlers to work.

A State of Emergency has been in force in Timaru in the South Island since late on Wednesday because of the risk of flooding after a levee was damaged forcing the evacuation of nearby houses.

In Christchurch, residents were having to deal with surface flooding and more than 300 households are without power after two power poles fell across the road, according to power company Orion Group.