South-east Queensland residents are waking to flooding across the region after an overnight storm dumped up to 250 millimetres of rain.

Roads are cut and powerlines are down across an area taking in Toowoomba, Brisbane and the Gold Coast, and one woman is unaccounted for.

The woman went missing in Enoggera Creek at Newmarket. A boat was found and her friend has been taken to the Royal Brisbane Hospital. He said he could not find her at the height of the flooding.

Energex says it is working to restore power to about 6,000 customers across the south-east.

Mike Swanston from Energex says fairly large branches have been carried on to powerlines on Paddington and Rosalie.

Power is off is also off in the Wynnum area.

Schools around The Gap have been described as "emergency supervision" only. Although schools remain open parents have been asked to make other arrangements if possible.

Weather bureau senior forecaster Geoff Doueal says some of the heaviest falls have occurred over Brisbane's three major dams.

"We have a seen a large area of heavy rain moving across the south-east during the evening and now it's over the Brisbane area," he said.

"Some places have had well over 100 millimetres of rain, so there is strong wind warnings for that, there is road weather warnings and we are continuing the warnings for flash flooding with lots of dangerous flooding out there considering the very heavy rainfall we have had."

Homes have been unroofed and cars have seriously damaged at Paddington in Brisbane's inner city.

North Regional Police Inspector David Richards said the extent of last night's storm damage was becoming apparent as the sun began to rise.

"It started off in the Gap area - a number of houses evacuated and the flooding went down quickly," he said.

"As quick as it came, it moved on through the Paddington area - a violent storm there unroofed four houses, knocked some powerlines down and there was a major number of vehicles affected by floodwater."

Flooding

Police are currently responding to reports of widespread flooding in areas across Brisbane south and west.

Primary areas affected include Ipswich, Oxley, Darra and Forest Lake plus the Gap, Ashgrove, Sherwood and Indooroopilly.

Boats have been used to patrol streets in Newmarket. People have been asked to not go on the roads, in order to let emergency services personnel work.

Emergency services have also asked the people do not run in the brown water that is filling streets.

Police say suburban roads and major highways are cut around the south-east.

RACQ spokesman Joe Fitzgerald says residents should stay home if possible.

"Only essential travel - if anyone does need to get somewhere they need to kind of second guess themselves as to how important that travel is and maybe staying in for the time being might be the best option cause the roads are pretty chaotic," he said.

At Ipswich - where the heaviest falls were recorded - the Bremer River has broken its banks and Ipswich Mayor Paul Pisasle has described the flooding as the worst since 1974.

Emergency Management Queensland say scores of people have been rescued from cars that have been caught out by rapidly rising flood waters.

In Brisbane and Logan City, at least five motorists were rescued after they tried to drive through flooded roads on the Inner City bypass, at the Gap and Slacks Creek to the south.

Nine people were rescued in the Ipswich area at Woolshed Creek, Maudsland and Forestdale.

Mr Doueal says more storms are on the way.

"They won't be anything near the intensity, we don't believe, as last night's storm because that upper support's not there," he said.

"It's just more bad news for those still trying to clean up after Sunday's devastating storm."

Authorities are repeating strong advice to stay at home if possible. Avoid travelling unless it is essential to do so. There are predictions of further rain later this morning.

Trains

The Ipswich line is closed between Rosewood and Dinmore.

There will be no trains in this section in the morning peak hour, and possibly the afternoon peak hour (to be advised).

There is damage to signalling and track washed out in several places.

There is also water over the line between Ipswich and Toowoomba.

Translink says that rail buses (in place of trains) are operating this morning.

Buses will operate between Ipswich and Rosewood.

Buses will also operate between Ferny Grove Station and Keperra due to track damage.

All buses services are expected to keep running, although routes will be affected by closed roads.

Motorists are advised to not attempt to drive through flood waters as the depth may be deceptive and conditions may be dangerous.