The regional Investigative Committee said three people, including the director of the Listvyazhnaya mine and his deputy, had been arrested on suspicion of violating industrial safety rules.
It said miners had suffocated when a ventilation shaft became filled with gas. State television said prosecutors believed there had been a methane explosion.
The dead comprised 11 miners already confirmed killed, 35 who had been reported missing, and the six rescue workers.
Dozens of people were treated in hospital, at least some of them for smoke inhalation. Four were in critical condition.
The coal-producing region of Kemerovo, roughly 3,500 km (2,200 miles) east of Moscow, has suffered fatal mining accidents for years.
The Listvyazhnaya mine is part of SDS-Holding, owned by the privately held Siberian Business Union. The owner had no immediate comment.
Some 285 people were inside the mine when smoke spread through the ventilation shaft, the Emergencies Ministry said. Authorities said 239 had made it to the surface.
Kemerovo declared three days of mourning.
In 2007, the region was the site of the worst mining accident since the collapse of the Soviet Union when an explosion at the Ulyanovskaya mine claimed the lives of more than 100 people. In 2010, explosions at the region’s Raspadskaya mine killed more than 90 people.