BECKLEY, W.Va.—A federal judge sentenced a former Massey Energy Co. security chief to three years in prison Wednesday for obstructing a criminal probe into the 2010 explosion that killed 29 miners in the worst U.S. coal-mining disaster in four decades.

A jury in October convicted Hughie Elbert Stover of lying to federal investigators about a company policy of providing advance notice of federal inspections, and of obstructing a federal criminal investigation of the blast by ordering the destruction of more than 50,000 documents....