Flood-ravaged Fiji began a massive clean-up Tuesday, as the South Pacific nation's stretched health services expressed fears disease could quickly spread through evacuation centres.

At least three people have died in the floods, although local media reports, which police said they could not confirm, put the death toll as high as seven.

As tourist flights to the island nation resumed, some people were able to regain a semblance of normality as shopkeepers took advantage of a break in the heavy rains to begin cleaning up their properties to prepare for reopening.

But there were growing fears about conditions in evacuation camps housing 12,000 people forced from their homes, with health authorities concentrating on preventing an outbreak of communicable diseases.

"We are seriously concerned about the state of evacuation centres," Western Division health inspector Dip Chand told the Fiji Times.

"We have to put in place strategies that will prevent outbreaks and contain diseases if they do exist at these centres. We have to ensure that we do not reach crisis level."

Teams were issuing water purification tablets at the camps on the main island Vita Levu and inspecting sanitary conditions for those sheltering in them.

At Nadi township, businessman Riyaz Ali said the situation was bleak as locals came to terms with the scale of the devastating flood that had left their home looking "like a war zone".

"It's not a sight for the faint-hearted, the devastation is utter and complete," he told news website fijivillage.com.

"There's nothing left in most homes and you can see the look of desperation in people's eyes, it's just gut-wrenching."

In a rare piece of good news for the country, still struggling to recover from floods in January that claimed 11 lives, a cyclone warning was lifted after Tropical Cyclone Daphne missed the islands and moved further out to sea.

National carrier Air Pacific resumed inbound international flights to Nadi airport for the first time in three days.

Officials in Canberra said about 2,000 Australian tourists were still stranded in Fiji and Qantas had agreed to increase capacity on its flights to help them home.

New Zealand Foreign Minister Murray McCully said his government was donating NZ$500,000 ($413,000) to flood relief efforts, while Australia contributed Aus$1 million (US$1.04 million) on Monday.

Both countries have tense diplomatic relations with Fiji's military government, which seized power in a 2006 coup, but stress the money would go to aid agencies rather than military strongman Voreqe Bainimarama's regime.