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