A group of up to ten workers were within metres of the incident and tried to render first aid on the man, CFMEU boss Dean Hall said.

He said the man died when a mobile crane rolled over while moving a large generator at a low height.

"During that process it's gone catastrophically wrong, [the crane] rolled on its side, and as a result, the boom ... which was lifting the generator has struck, fatally injuring the construction worker."

He said the crane was only a few months old.

Police were called to the site on Aikman Drive in Belconnen about 6.40pm.

The site was blocked off by police on Thursday night, with a police vehicle guarding the entrance.

Officers, paramedics and Worksafe staff were seen at the site and several people could be seen inspecting an area near what appeared to be a crane on its side.

The site remained closed on Friday morning while the fatality was being investigated by ACT Policing.

Mr Hall said the man who died was a union member and a contractor with Brookfield Multiplex, the company designing and constructing the new hospital.

He said everyone was working together to work out what went wrong as there were "a lot of factors at play".

"We owe that to the worker and his family and so we can try to stop it happening in the future," he said.

Chief Minister Andrew Barr said the man's death was a "terrible tragedy" and there would be a full investigation into what occurred.

"I express my deepest condolences to the family and friends of the worker who lost his life. Our thoughts are with them and all his colleagues at the site," he said.

"The government will do everything it can to assist the police and Worksafe. They will comment further on the detail of this tragic incident at the appropriate time."

In a statement, Brookfield Multiplex said emergency procedures were actioned and an ambulance "immediately attended" the site.

The site was then stabilised. "There is no ongoing risk to anyone else on site," the statement said.

Brookfield Multiplex regional managing director David Ghannoum said the company was "working hard to uncover what has happened and we will share more details when we can".

"Our sincerest thoughts and condolences go out to the family and co-workers of the deceased," he said.

ACT Policing's Criminal Investigations Team and Worksafe ACT are investigating the death and a report will now be prepared for the coroner.

Construction on Canberra's newest public hospital only began in February. The $139 million development is expected to be finished in 2018.

Thursday's fatality comes only days after it was confirmed that a large crane at the site, not the one involved in the incident, was recently temporarily shut down due to safety concerns.

Worksafe had issued a prohibition notice to fix a "spooling issue" where a cable was not correctly wrapped or stored onto a drum, but on Tuesday, Worksafe said it had been fixed and the notice lifted, with the crane again operational.

The notice was issued after a Worksafe audit of cranes in the ACT.

Mr Hall said it was important to "pay the appropriate respect to the safety needed on construction sites".

"Unfortunately when it goes wrong, it goes horribly wrong and when you have a workplace accident in a construction site, you don't get a paper cut, you get serious and often life-ending injuries. Unfortunately we have seen that happen here."

He urged anyone who worked on the site or knew the worker to contact CFMEU, which provides a free, confidential counselling service for members and non-members.

"They should contact us because there will be a lot of people out there who have experienced fatalities before or been involved in accidents or have known the worker and today may bring back those memories," he said.

"If they need help we can get it for them."

The University of Canberra offered condolences to the man's family, loved ones and colleagues.

"We are saddened by the news of the worker who lost his life at the construction site yesterday evening," acting Vice-Chancellor Professor Frances Shannon said.