EX-TROPICAL Cyclone Penny sits close to the coast near Bowen.

The Bureau of Meteorology forecast has a trough associated with the system expected to move northwards during the next 24 to 36 hours.

A severe weather warning for heavy rainfall remains in place for the Central Coast and Whitsundays forecast districts, along with Herbert and Lower Burdekin, Northern Goldfields and Upper Flinders.

Despite the proximity of Penny to Bowen, the town received 12.4mm of rain up until 9am on Wednesday and 4.4mm between 9am and 5.30pm on Wednesday.

Falls have been heavier in the southern parts of the Whitsundays region.

Preston, near Proserpine, recorded 167mm in the six hours to 2am on Wednesday, while 107mm fell in the same timeframe in Prospect Creek, west of Koumala.

A total of 110mm was recorded at Myrtlevale.

Proserpine received 80mm in the 24 hours leading up to 9am, but only a further 1.4mm has fallen up until 5.30pm.

Hamilton Island received 78.2mm up until 7.30am, with 25.6mm falling in less than an hour from 9am on Tuesday night.

The popular holiday destination has had a maximum wind gust of 83km/h.

An unofficial BoM reading recorded 97mm of rainfall in Cannonvale up until 9am Wednesday morning and 74mm in Jubilee Pocket.

Hamilton Plains received light flooding, but the road is still safe for motorists and the Whitsunday Regional Airport has been operating as normal.

BoM meteorologist Gordon Banks said the bureau would cease using the track map, as once the system moved inland, it became difficult to track.

"It's pretty weak now. It doesn't even have strong winds around it, let alone gales, but it is still generating plenty of rainfall," he said.

In the BoM's latest update, released at 4.50pm on Wednesday, heavy rain, which may lead to flash flooding, is expected to occur on Wednesday night and Thursday in coast and adjacent inland areas between Mackay and Rollingstone, particularly with thunderstorms.

Locations that may be affected include Bowen, Proserpine, Ayr, Charters Towers, Townsville and Rollingstone, with isolated six-hour rainfall totals between 150mm and 180mm possible.

A flood watch remains in place for coastal catchments between Proserpine and Cape Tribulation.

Catchments likely to be affected include the Burdekin River, downstream of Burdekin Falls Dam, Proserpine River and Don River.