Fijian Prime Minister Frank Bainimarama says he expects fatalities from super-cyclone Yasa to rise.

A 45-year-old man and a three-month-old baby have been confirmed dead after the category 5 storm swept through the country.

"We sadly expect fatalities to rise," Prime Minister Bainimarama said on Friday evening.

Yasa swept through the Bua Province of Vanua Levu with wind speeds up to 345km/h.

"It tore across Vanua Levu through the night, exiting Sawani, and then sweeping across the central Lau group," Bainimarama said.

"Its strength has dropped to category 3 and it is currently heading southeast."

Vasiti Soko, director for the National Disaster Management Office, says it could cost "hundreds of millions" in damages. 

"We will continue to assess the scale of damage in the coming days."

Despite this uncertainty, Bainimara is urging the country to stay strong.

"These storms may be getting stronger, but they will never be stronger than we are," he said.

"Resilience is in our bones. This is our home, and we will recover, we will rebuild, we will prove ourselves stronger than Yasa.

"Stay strong, Fiji. We will prevail once again."