A miner trapped underground after a mine collapse at Ballarat has died.

Two miners were pinned by fallen rocks at the mine on Woolshed Gully Drive at Mount Clear, northwest of Melbourne, on Wednesday afternoon.

Officers were called to the mine site just before 5pm.

While 28 workers were able to take refuge in a safety pod, a 21-year-old Ballarat man was stabilised before he was taken out of the mine about 8.30 pm on Wednesday with lower body injuries, Victoria Police said.

He was later flown to a hospital in a life-threatening condition.

Police on Thursday morning recovered the body of a second trapped man, aged 37, from Bruthen, east of Bairnsdale, who died after the rockfall.

"The incident occurred approximately 3km underground from the mine entry," Victoria Police said in a statement.

Australian Workers Union Victoria state secretary Ronnie Hayden said some workers had flagged concerns about the mine before the incident took place.

"Our members have raised concerns about this style of mining and it seems to have fallen on deaf ears," he said. 

"Me, personally, I believe this is the fault of management - but that will be left to investigators."

The union was called to the mine after the men were trapped underground about 5pm on Wednesday.

The two workers were undertaking a manual type of mining called air legging which was a new activity on an old site, Mr Hayden said.

"They were working on unsupported ground, trapping both miners and killing one," he said.

"It's devastating because we've lost another worker."

Mr Hayden said the style of mining taking place was not appropriate for the setting.

"This form of air legging should not be used to do this type of work," he said.

"The information we're getting back was this was a quick, cheap and easy way to chase gold."

Federal Minister for Resources Madeleine King said it was too soon to have a solid idea of what caused the incident.

"Oh, look, it's too early to really go into any speculation about what's happened at that mine," she told ABC Radio. 

The miners who were able to take refuge in a safety pod after the collapse were successfully brought to the surface a short time later.

WorkSafe will investigate the incident and police will prepare a report for the coroner.

The mine's owner Victory Mineral said its emergency response team was working closely with Victoria Police and other authorities.

"Right now our priority is the safety and well-being of our mining workers and their families," it said in a statement.

Victory Minerals took operational control of the Ballarat Goldmine in December 2023. 

"We bring significant experience and expertise to the mine," it said. 

"We are a safety-first mine operator and respect the work that underground miners perform every day."

The mine's website states it has an extensive network of tunnels and operates deep beneath buildings, streets and homes.

Ballarat Mayor Des Hudson said the miner's death was devastating news.

"We are a very resilient community," he said.

"There will be great community concern and support by the local community to those that are involved."

In 2007, 27 miners were trapped underground at the mine for several hours before being winched to safety.

The suburb of Mount Clear was also the focus of the search for mother-of-three Samantha Murphy, who police allege was murdered by 22-year-old Patrick Orren Stephenson.

The Project with AAP.