"The owner and administration of the mine has repeatedly allowed violations of safety conditions of mine operation," the agency said.
It warned that the Yuzhkuzbassugol might be stripped of its licence.
Below the surface
The explosion occurred about 520 metres below the surface at the mine around 7:30am local time (0330GMT).
A total of 179 miners were either brought to the surface or made it out on their own, emergency department spokeswoman Natalia Lukash said.
Irina Andrianova, another emergency department spokeswoman, said 217 people had been working in the mine at the time of the blast.
Her statement that the death toll had risen to 38 appeared to account for all those who had been in the mine.
Aman Tuleev, governor of the Kemerovo region where the mine is located, said the blast may have been caused by the collapse of a coal wall where drilling was taking place.
Workers' safety
Tuleev called for a change in ownership of the mine, saying: "The owners of the mine answer for the safety of our mine workers.
"If we can't change the company owners, then we will try to revoke the licence of the company."
Yuzhkuzbassugol's ownership is split evenly between the company's management and coal and steel producer Evraz SA, which is partly owned by billionaire Roman Abramovich and which acquired its 50 per cent stake in December 2005.
The blast comes just over two months after 110 people died in a methane explosion at the Ulyanovskaya mine in the same region, known as the Kuzbass.
That blast was the worst accident in more than 60 years in Russia's mines.
Strategy review
In a statement posted on its website, Evraz said it was reviewing its business strategy of investment in Yuzhkuzbassugol, which is a major supplier of coking coal to two Evraz steel mills.
"Aside from this, Evraz, for its part, will review all possibilities for reducing the levels of technological and industrial risks in this coal company," the company said.
On Tuesday, Rostekhnadzor fired or suspended five regional officials in connection with the March blast at the Ulyanovskaya mine.