A truck driver is in hospital with serious injuries after his semi-trailer and two passenger trains crashed on Brisbane's northside this morning.

The oversize truck was carrying a 38-tonne transformer but bottomed-out on the level crossing at Banyo station at 6:30am (AEST).

As the driver tried to jack it from the tracks, the truck was hit by a northbound train and thrown into another passenger train waiting at the station.

The truck driver was seriously injured and received CPR at the scene before being taken to Royal Brisbane Hospital.

Around 15 train passengers were treated at the scene for minor injuries.

Ambulance officer Matt Hannabery says the truck driver had been desperately trying to jack the truck off the tracks.

"His injuries were isolated from his pelvis down, so all lower leg injuries, but they are serious injuries," he said.

Police Inspector Mark Laing says the truck had been carrying a 38-tonne electrical transformer.

"It would appear that the prime mover itself was across the tracks," he said.

"There was some difficulty in respect to the trailer getting over the ridge.

"As a consequence, a northbound train from the city to Caboolture has [crashed] with the semi-trailer."

Horrific noise

Commuter Chris Harman had been in the train waiting at the station when the crash happened.

"We all heard it and then we had a few announcements put over the PA system of the train fairly quickly and then after that we were all told to get off the train because the powerlines on the platform were damaged," he said.

Mr Harman said the truck was wedged between two trains.

Linda O'Leary had a family member involved.

"The noise was horrific she said and she was in the front carriage so she was pretty shaken up," Ms O'Leary said.

The Shorncliffe line will be closed for much of the afternoon as the clean-up continues.

The State Government says the rail safety regulator will investigate the crash.

Queensland Rail (QR) says it is lucky no-one was killed.

"Eleven customers on board and a train driver and a guard have all been tended to by Queensland ambulance services and are continuing on their way," spokesman Martin Ryan said.

"The train driver is very shaken and is back at Queensland Rail under care."

Labor Councillor Kim Flesser says he has been trying for several months to come up with a plan to make the crossing safer.

"The Lord Mayor and councillors on his side of the chamber blocked the motion," he said.

"They didn't support it and said basically we are not going to do anything."

Queensland Rail spokesman Martin Ryan says the company is investigating what went wrong.

"This did have boom gates and signals with lights flashing," he said.

Buses are replacing trains between Northgate and Shorncliffe tonight.