Doctors have warned an upgraded patient records system being rolled out at Queensland hospitals is plagued by dangerous flaws.

A new IT system being rolled out at Queensland hospitals is dangerous and must be halted to protect patients, the Australian Medical Association of Queensland has warned.

The ABC has obtained a letter from the AMAQ urging health and hospital services to halt the rollout of an upgraded patient records system, which is already being used at 10 hospitals.

It says the system is plagued by lags, resulting in patients being given multiple doses of drugs, and data such as heart rate and oxygen levels not being recorded during surgery.

Patient data has also gone missing, the AMAQ says.

More than 40 safety alerts regarding issues with the Integrated Electronic Medical Record (ieMR) system have been sent to Queensland hospitals over the past year, the ABC reports.

"We believe an urgent pause to the rollout is needed to reduce overloading a strained network, and stop problems spreading and impacting on patient safety and productivity," AMAQ president Dilip Dhupelia wrote in the letter.

Queensland Health says its working with the AMAQ, saying concerns it had raised "were either noted as resolved, required further clarification, or assurances/feedback was provided regarding the claims".

"Our priority is patient safety and care and we are confident this has not been compromised," a spokesman told the ABC.