The regional investigation team said three people, including the director of the Listviajnaya mine and his deputy, were arrested on suspicion of violating industrial safety rules.
It said the miners suffocated as the ventilation shaft was filled with gas. State television said prosecutors believed a methane explosion had occurred.
The dead included 11 miners who had already been confirmed, 35 missing and six rescue workers.
Dozens of people were treated at the hospital, some of them for inhaling smoke. Four people were in critical condition.
Kemerovo’s coal-producing area, about 3,500 km (2,200 miles) east of Moscow, has been plagued by dangerous mining for years.
Listvyazhnaya mine is part of SDS-Holding, which is privately owned by the Siberian Chamber of Commerce. The owner made no immediate comment.
The emergency ministry said about 285 people were inside the mine when the smoke spread through the vents. Authorities said 239 had reached the surface.
President Vladimir Putin said he had spoken with the governor and emergency officials, and ordered the Kremlin to fly to the region to assist the emergency minister.
Kemerovo declared three days of mourning.
In 2007, after the collapse of the Soviet Union, an explosion at the Ulyanovskaya mine killed more than 100 people, and the area became the site of the worst mining accident. In 2010, more than 90 people were killed in explosions at the Raspatskaya mine in the region.
“Communicator. Music aficionado. Certified bacon trailblazer. Travel advocate. Subtly charming social media fanatic.”