At least 16 people have died in flooding in the Solomon Islands, while 40 are missing and up to 49,000 homeless, an aid official said Saturday as the full extent of the devastation began to emerge.

The disaster has raised fears that a lack of sanitation and fresh water will lead to an outbreak of dengue fever in the Pacific Island nation.

"It's grown a lot worse," Save the Children's emergencies manager Graham Kenna told AFP as reports filtered in of the havoc outside the capital Honiara.

Initial reports from the capital indicated nine dead and 10,000 homeless but the picture became more grim as contact was made with outlying areas.

"The last report we had was there are 16 in the mortuary and at least 40 still missing, most of them children and it's very unlikely they'll be found alive," Kenna said.

"There are 49,000 who have lost their homes and are seeking temporary shelter."

At Honiara's National Referral Hospital the mortuary is already full and a refrigerated container has been placed in the car park to handle the growing number of bodies.

"It is a sad time for many families and also so much stress as they lose not only loved ones but their whole livelihoods too," doctor Alex Munamua said.

Kenna said aid agencies urgently needed tents and tarpaulins but they could not be flown in while the airport remained shut after two houses floated onto the runway.

- 'A tragedy none saw coming' -

The Red Cross secretary general in the Solomons, Joanne Zoleveke, described the devastation as "a tragedy none of us saw coming".

The city's main river, the Matanikau, burst its banks in a torrential tropical storm late Thursday, sweeping away riverside communities, bringing down bridges and inundating the downtown area.

"We were watching the river but never expected it to rise so fast. It took us by surprise. That is why there are deaths," Zoleveke said.

Local resident Paul Lega told the Solomon Star newspaper the river rose too fast for some families to escape.

"I witnessed a mother and two children swept away in their home," he said as the newspaper described the devastation as "the worst disaster the nation has seen".

World Vision's Emergency Response Manager in the Solomon Islands, Lawrence Hillary, told Fairfax News the organisation was particularly concerned about the welfare of children.

"My staff has witnessed a child being swept away by the floodwaters. They are devastated by what they have witnessed."

Aid workers feared outbreaks of disease in the sodden city and were waiting for Honiara's Henderson International Airport to reopen so emergency relief supplies could be flown in.

"Thousands of people are living in schools and other cramped conditions with poor sanitation and relying on rainwater for drinking," Kenna said.

"We expect an outbreak of dengue fever in two weeks," Kenna said.

The flooding had cut off roads throughout Honiara and of the two main bridges crossing the Matanikau, one was washed away and the other was closed after large cracks appeared in the structure.

The loss of the bridges prevented officials seeing the scale of destruction caused by landslides and floods in outlying areas although a helicopter had been able to make reconnaissance flights from Honiara.

As Solomon Islanders battled the floodwaters they were also shaken by a strong 6.0 magnitude earthquake late on Friday, but there were no reports of any damage.