Far north Queensland is bracing for a second natural disaster in barely a month while flooding has forced people to flee their homes in the Northern Territory.

Intensifying activity in the Coral Sea is expected to result in the formation of Cyclone Kirrily by the end of Sunday.

The cyclone won't be officially named until it is properly formed, the Bureau of Meteorology's Dean Narramore told AAP on Saturday.

"It is still maybe a day away from becoming a cyclone and mid next week it is looking like tracking towards the Queensland coast," he said.

Exactly where the cyclone could cross the coast is unknown, but Mr Narramore predicted between Cairns and Mackay among a "range of scenarios".

"In terms of how strong it will be and what time it will reach land ... it's too early to say."

Updated forecasts on Saturday maintained expectations of intense rain leading to flash flooding, linked to a monsoon trough across the southern Carpentaria.

The heaviest fall in the past 24 hours was 158mm recorded at Whyanbeel Valley, near Port Douglas, while up to 180mm in six hours is possible as the result of a slow-moving tropical low close to Elliott in central NT.

"There is a very widespread flood watch across the Kimberley near the Northern Territory and much of the (Cape York) Peninsula of Queensland," Mr Narramore said.

Major transport and freight route, the Stuart Highway, is closed at two locations, including between Tennant Creek and Devil Marbles turn-off, with the centre receiving another 100mm of rain in the past 24 hours.

"Locally, intense rainfall which may lead to dangerous and life-threatening flash flooding is also possible with thunderstorms in western and northern parts of the Barkly district, including Tennant Creek, and in the far eastern Gregory district," the Bureau of Meteorology reported.

There is a general flood warning for the NT's Victoria River catchment after almost 100 people were evacuated, with more to come.

Motorists have been stranded, roads cut and people evacuated in the NT with about 40 from Pigeon Hole, a Bilinara Aboriginal Land Trust settlement, relocated while another 50 at nearby Daguragu left for Kalkarindji.

Pigeon Hole could be flooded for up to a week.

The low is expected to push toward the Western Australia border, bringing wind and rain to northern parts of the Kimberley.

In positive news, the Captain Cook Highway between Cairns and Port Douglas reopened to traffic on Saturday following damage caused by December's ex-Tropical Cyclone Jasper.

Scores of landslips damaged the highway and multiple culverts were blocked or needed repair, with crews removing large amounts of mud and debris.

Some Queensland Rail services remain impacted, Queensland's acting Transport Minister Scott Stewart said.

"Significant progress has been made onsite with 39 of the 61 damaged sites now cleared to allow access for work trains to begin removing soil from the area," he said.

Australian Associated Press