A weakened Cyclone Ita could dump up to 300mm of rain on populated coastal communities in central Queensland as the storm heads south.
The category one storm, which crossed the coast north of Cooktown as a category four storm on Friday, was 20 kilometres southwest of Port Douglas at 5pm on Saturday.
As the storm rumbles south, Premier Campbell Newman has urged Queenslanders to work together as recovery agencies begin to reach communities battered by Ita.
The weather bureau says Ita remains at category one strength with wind gusts of up to 120km/h set to batter populated areas from Port Douglas to Cairns, extending to Innisfail on Saturday evening, and could be felt as far south as Townsville on Sunday.
Strong winds could also extend to Proserpine on Sunday if Ita heads offshore.
Heavy rain of up to 300mm could hit areas from Port Douglas to Ayr, the bureau warns.
A spokeswoman from Cairns Regional Council urged residents to remain indoors when the cyclone passed on Saturday evening as there was a risk of strong winds and flooding to low-lying areas.
A cyclone warning remains between Cape Tribulation and Proserpine and storm surges between Cape Tribulation and Cairns are possible.
Rain is expected to ease along the Daintree River, north of Port Douglas, which peaked at 10 metres above flood levels on Saturday after the area was hit with 400mm of rain.
The storm crossed the coast as a category four cyclone at Cape Flattery, north of Cooktown, about 9pm on Friday before weakening as it headed south.
Three children and their parents have been rescued from fast-flowing floodwaters in Cooktown.
''Great work by QFES Swiftwater & SES floodboat crews! 2 adults & 3 children rescued from floodwaters 10km sth of #Cooktown. #TCIta,'' Queensland Fire and Emergency Services commissioner Lee Johnson tweeted.
Residents in Cooktown had a sleepless night as intense gales and heavy rain battered the town, uprooting large gums, tearing down powerlines and scattering tin and other debris across roads.
Roofs were ripped off two homes and a pub in Cooktown and two buildings were significantly damaged in Hope Vale, but the far north was relatively unscathed.
Cooktown remains isolated by flooding and authorities say it could be cut off for days.
Power had been restored to most areas of Cooktown, but Hope Vale remains without power and mobile phone service.
Floods have isolated the small community of Wujal Wujal, south of Cooktown, but buildings in the town received only minor damage despite storm surges up to two metres.
Mr Newman said there had been no reported deaths or injuries in the cyclone, but roads are cut to many affected communities including Cooktown and Hope Vale impassable, hampering recovery efforts at this stage.
"We all want to get there as soon as possible to help out, to put things back together, to clean up, but frankly this event is still occurring. This is still a cyclone," he said.
"There are real difficulties getting into certain areas, so I am asking Queenslanders to work together as a team to get through this event."