Australia will be better prepared to treat trauma patients in the event of a national emergency after a new agreement was signed between Queensland and the Northern Territory.

The federal government has provided $50 million until 2013 to fund a new partnership between Brisbane's Princess Alexandra Hospital (PAH) and the Royal Darwin Hospital's National Critical Care and Trauma Response Centre.

Under the agreement, PAH will be able to deploy up to 40 additional medical staff to Darwin when a disaster strikes.

Federal Health Minister Nicola Roxon, who was in Brisbane on Thursday to announce the agreement, said Australia would be more prepared than ever when a natural disaster or terrorist activity hit northern Australia or the Asia Pacific region.

Queensland's Health Minister Paul Lucas said both hospitals would work together to train staff in trauma patient care.

"When a disaster strikes this means we can stick people on a plane immediately who are familiar and know that Darwin hospital backwards so they can get in there and get stuck into treating patients," Mr Lucas said.

"We know these sorts of disasters and terrorist events will happen again."

The trauma centre was born out of the Bali bombings in 2002 where many of the patients, foreign and Australian, were taken to the Royal Darwin Hospital.

Since then it has had to respond to several disasters in the region, including the boat explosion off Ashmore Reef in April this year.

NT Health Minister Kon Vatskalis said Darwin was a strategic location and played a critical role in caring for trauma patients.

"Darwin is in a situation to evacuate people and it is the ideal location to stabilise people, but what we want to do is create a pool of doctors and nurses who we can draw upon when these disasters happen," Mr Vatskalis said.