Roger Nicholson, senior vice president of International Coal Group which owns the Sago mine located near the town of Tallmansville, said the explosion occurred at about 6.30am (1130 GMT) as a work crew went underground to resume operations after the New Year's holiday.
A second crew consisting of six men who descended into the shaft soon after heard the explosion but ran into collapsed rock and decided to retreat without making contact with their comrades.
"As a result 13 underground miners are presently unaccounted for," Mr Nicholson said.
He said that attempts to communicate with the missing men have so far been unsuccessful.
At least five professional rescue teams are already on the scene and more are on their way, according to Mr Nicholson.
But a rescue operation has been delayed by methane gas seeping into the mine and making it impossible for rescuers to immediately go underground, according to local officials.
They waited for the gas to be pumped out to begin their work without putting their own lives in danger.
Rescue work is also being complicated by the fact that the Sago mine lies about 1.6 kilometres below ground.
Mr Nicholson said the cause of the explosion is not yet clear but said that "it occurred simultaneously with a very heavy thunderstorm in the region."
West Virginia Governor Joe Manchin said he was heading to the scene of the accident to coordinate rescue work.
West Virginia has large reserves of coal, and mines have operated in the region since the early 1800s.