A man has been killed in Vanuatu as Tropical Cyclone Lusi passes over the Pacific nation.

Authorities say the man was killed by a falling branch on Pentecost Island in Penama province on Monday.

The category two cyclone has also caused flooding and destroyed houses and crops on several islands in Vanuatu.

Vanuatu National Disaster Management Office Philip Leto said people are still fleeing to evacuation centres as the bad weather moves south.

"Most of the people have evacuated to evacuation centres not knowing whether their houses are damaged," Mr Leto said.

"Also, these people are living in traditional houses and traditional houses are built with local materials so they might not believe in those houses."

A cyclone warning remains in place.

Audio: Vanuatu National Disaster Management Office Philip Leto speaks to Pacific Beat. (ABC News)