Hughie Morton, 21, and Troy Mathieson, 23, were last seen on Ross River Road, near floodwaters on Tuesday morning.

The pair have not been located despite extensive inquiries with family and friends and a search of floodwaters and the area has begun as a precaution, police say.

Rain was still coming on Monday as emergency workers used boats, choppers and tip-trucks to rescue well over 1000 residents from Townsville's flooded suburbs.

They were helped by many other citizen heroes including some in an armada of fishermen's tinnies who braved the murky snake and croc-filled floodwaters to help their neighbours.

Scenes from the floodwaters show grim-faced residents carrying pets and whatever they could as they waded to dry land.

The vigorous monsoon trough dumping the rain has begun moving south but it is unpredictable and dangerous conditions are expected to continue for at least the next 24 hours.

About 1000 people remain in six evacuation centres but some residents are refusing to leave their homes.

In flooded Hermit Park, near the city centre, Andrew Roberts says he and his wife, Cass, have food, water, and a radio - and won't be leaving their two-storey home of 14 years.

"It's a little bit scary because when it floods in Townsville, the crocs get into the water," Mr Roberts told AAP.

"My biggest concern is getting eaten."

It makes crossing the murky water in their house to refuel the generator a hair-raising experience, he said.

Between 400 and 500 homes have been inundated by floodwaters in Townsville, although there are fears 2000 more may have been damaged by water.

Authorities are monitoring rainfall every five minutes at sites across the city so they can issue new alerts if there's a new threat to public safety but so far no lives have been lost.

Earlier, Townsville Mayor Jenny Hill batted away criticism from some residents that they were caught out by record water releases from the city's swollen Ross River Dam.

"We door-knocked for three days. Some people were door-knocked twice. You can't say you weren't warned that something could happen," she said.

A severe weather warning remains in place from Ingham to Mackay and west to Cloncurry, although lower than expected rainfall throughout Monday has eased conditions in Townsville.

Water levels in the Ross River Dam dropped to 213 per cent of capacity late on Monday, down from 250 per cent earlier in the day.

Further heavy rainfall is likely to develop in the severe warning area on Tuesday, with six-hourly rainfall totals between 150mm to 200mm possible, the Bureau of Meteorology has says.

Creek and river catchments are already saturated and will respond extremely rapidly to any rainfall, a spokesman said.

Australian Associated Press