The ministry said a combustible mixture of gas and air fueled the explosion at the Karl Marx mine in eastern Ukraine, RIA Novosti reported.
"Three miners who were on the surface were injured in the blast, while the fate of 40 who were working underground remains unknown," the ministry said.
ITAR-TASS reported the explosion in Yenakiyevo had also destroyed the mine shaft's surface structure, which allows air to be pumped into the underground mine.
The Russian news agency said both rescue and medical workers were on their way to the mine accident site.
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