Officials in Samoa confirmed two deaths on Friday in the wake of Cyclone Evan and warned the storm was heading back to the capital Apia, which has already been hit by power cuts and flash flooding.

The cyclone, described by witnesses as the worst in decades, hit the Pacific island nation on Thursday afternoon, uprooting trees, bringing down power lines and flooding much of the city centre.

Hundreds of people were forced to seek shelter in evacuation centres as high winds tore roofs off homes and the Vaisigano river, which runs through the centre of the capital, burst its banks.

A Disaster Management Office spokeswoman said there had been at least two confirmed deaths, while media reported a number of children were missing after being swept away by the raging river.

"This is the biggest one I've been through and I've been through difficult situations in the Pacific (before)," New Zealand's high commissioner in Apia, Nick Hurley, told Radio New Zealand.

"The unpredictable nature of this one has made it quite different. The forecast winds did not give any indication of how strong the impact was going to be."

The Samoa Meteorological Service said that after heading out to sea, Cyclone Evan had wheeled around and was again bearing down on Apia.

A number of holiday resorts were reportedly flooded and the US embassy in Samoa has set up a hotline for citizens caught in the storm, advising them to move away from coastal areas.

In travel advice, the Australian government said the cyclone had caused "damage to local services and infrastructure, including communications and electricity services and Faleolo International Airport".

"The Australian High Commission in Apia has closed until further notice due to storm damage," it said.

The Fiji Meteorological Service has warned the cyclone could threaten northern parts of Tonga on Saturday and reach Fiji by Sunday.

AFP