The regional investigation 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 were suffocated when a ventilation shaft was filled with gas. State television said prosecutors believed there had been a methane explosion.
The dead included 11 miners who have already been confirmed killed, 35 who had been reported missing and the six rescue workers.
Dozens of people were treated at the hospital, at least some of them for inhaling smoke. Four were in critical condition.
The coal-producing region of Kemerovo, about 3,500 km (2,200 miles) east of Moscow, has been hit by fatal mining accidents for years.
The Listvyazhnaya mine is part of SDS-Holding, owned by the privately owned Siberian Business Union. The owner had no immediate comments.
About 285 people were inside the mine when the smoke spread through the ventilation shaft, the Ministry of Emergency Management said. Authorities said 239 had reached the surface.
President Vladimir Putin said he had spoken to the governor and emergency officials, and the Kremlin said he had ordered the emergency minister to fly to the region to help.
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 killed more than 100 people. In 2010, explosions at the region’s Raspadskaya mine killed more than 90 people.