Tropical Cyclone Imogen has crossed the Queensland coast, with huge falls recorded in parts of the far north and more to come.

The storm system was upgraded to a Tropical Cyclone while in the Gulf of Carpentaria Sunday afternoon.

Tropical Cyclone Imogen crossed Queensland shortly before 11pm to the north of Karumba.

It was moving southeast at 18km/h at the time.

A tropical cyclone warning was updated by the Bureau of Meteorology at 10.56pm, with the warning zone being from Burketown to Kowanyama, extending inland to Croydon.

The system is expected to turn into a low, but a severe weather warning is in place for areas from the far north to the lower Burdekin.

More than 260mm has fallen at Normanton since 9am yesterday, with falls of 192mm at Mornington Island and 75.6mm and 74mm at Burketown and Kowanyama.

The bureau warns that heavy rainfall that may lead to flash flooding will continue over the western Cape York Peninsula and will extend eastwards today.

Six hourly rainfall totals between 100mm to 150mm are likely near the low with localised intense falls up 200mm possible.

Heavy rain which may lead to flash flooding is also forecast to develop between Cooktown and Ingham, continuing into Tuesday, with six-hour rainfall of up to 200mm expected.

"Localised intense rainfall leading to life threatening flash flooding is also possible during this period, with six hourly totals of 250mm possible about the coast and ranges," the Bureau warns.

There are flooding warnings in place for the Belyando, Paroo, Bulloo, Thomson, Diamantina, Georgina, Lower Flinders, Norman and Gilbert Rivers.

There is a flood watch for parts of the top end, south to Ayr.

From Sunday afternoon and into the evening the cyclone had wind gusts up to 100kmh.

"Imogen is expected to continue moving east-southeastwards in the short term, taking it further inland tonight and Monday, and is expected to transition to a tropical low in the next few hours," the warning said.

"Longer term, the system is expected to track more slowly to the southeast over the southern Cape York Peninsula as a deep tropical low."

People between Burketown and Kowanyama, including Burketown, were advised to remain indoors until the cyclone has passed.

The Bureau said the tropical low would impact the state's far north for "the next few days".

Residents have been warned to brace for gale force winds, abnormally high tides, large waves and heavy rainfall.

The conditions may lead to flash flooding, the Bureau of Meteorology warned.

When the system passed over Mornington Island on Sunday, damaging winds and 200mm of rain were recorded.

Forecaster Matt Marshall said the heavy downpours were expected Monday and Tuesday.

"Isolated falls of a few hundred millimetres are possible on each day in coastal areas," he said.

"Heavy rainfall is also likely to lead to flooding in the flood watch area, which is the Gulf and north tropical coast, into the coming week."

Mr Marshall said southeast Queensland could be hit by thunderstorms on Tuesday or Wednesday.

Originally published as 'Life-threatening floods': Huge downpours as TC Imogen hits