An unexpected weather event has damaged properties and flooded roads in the Cook Islands while French Polynesia is dealing with the aftermath of huge swells.

Swells of up to 4.5 metres inundating coastal areas, driven by a high pressure system pushing up from New Zealand have been labelled a highly unusual weather event by Cook Islands' emergency management director.

John Strickland said the impacts were the most far reaching he had seen in a decade.

"It was a sudden hit at night, there was damage that took place Tuesday night local time," Strickland said.

He said there was an "unexpected sea surge" in Rarotonga.

"Rough seas, debris and rocks, you name it, it was shifted onto the road."

Low lying coastal areas in Puaikura District along with Titikaveka, in Takitumu District, were the most severely impacted areas.

"At the Rarotongan Hotel, guests were shifted from their rooms, because some of the rooms were on the beach," he said.

National emergency operation teams were activated from three vilages to support the infrastructure team as they were busy.

Strickland said while things have settled down, early on Thursday morning local time he received reports of northern Islands experiencing high seas, resulting in the closure of schools.

Emergency services remain on high alert and fresh warnings have been issued for the Northern parts of the Cook Islands.

A meeting is underway between Red Cross, police and other emergency teams.

Cook Islands' meteorological service director Arona Ngari said homes were evacuated in Titikaveka and Arorangi districts.

"There seems to be a couple of events that have exceeded expectations and that revolves around a couple of the high tides. So it is a pity, it is awful to see the damage from the high pressure system," he said.

Houses and roads submerged in French Polynesia

The level of the ocean surrounding French Polynesia has significantly risen and has submerged roads and houses bordering the oceans on the west coast of Tahiti.

La Premiere reported that 15 houses on the coast were submerged and the homeowners evacuated.

French Polynesia was battered this week by 8-9 metre swells.

All marine and water related activities are forbidden for most of the territory including going to the beach.

According to local meteorological authorities this is an "exceptional phenomenon" which hasn't been seen in French Polynesia since 2005.

A local fisherman Benjamin Tematahotoa said he is worried his boat will be lost in the flooding.

"Of course it's worrying, thats why we are staying vigilant and we are staying here," he said.

"If we really need to bring the boat back then we will tow it home. It's stressful especially if this is only the start. It's rising, it's rising, every five minutes, it's rising it looks like its going to keep rising".

La Premiere reported that two surfers were injured while attempting to surf during the high swells.