"The bodies of 89 miners have been recovered and all of them have been brought to the surface and sent for forensic examination. The fate of 11 miners is still unclear," the statement said.
An explosion early on Sunday in the Zasyadko coalmine in the Donetsk Region, the heart of the country's coal industry, caused a fire to rage through the mine. A total of 457 miners were underground at the time. 357 were brought up alive, with 34 of them later hospitalized.
Fires, smoke and falling rocks have hampered the search effort, dimming hopes that more miners could still be alive.
The mine resumed operations late on Wednesday following checks, Sergei Tulub, the Ukrainian coal minister said.
The Zasyadko coalmine is notorious for fatal accidents - a methane gas explosion killed 50 miners in 1999, with twenty dying in another explosion three years later. A gas leak at the mine killed 13 miners and injured dozens more in September 2006.
Wages at the majority of Ukrainian mines are calculated by coal volumes. This often leads miners to ignore safety procedures that could cause production lines to be halted.