The move comes about two months after solar panel maker Solyndra also filed for bankruptcy, setting off criticism of the government loan program.
The department guaranteed $535 million in loans to Solyndra, and Congress is investigating whether political influence played a role.
Beacon Power used the government-guaranteed-loan to build a 20-megawatt flywheel energy storage plant in Stephentown, New York.
The company said in documents filed with Delaware's bankruptcy court that it had $72 million in assets and $47 million in debts.
The case is Beacon Power Corp, U.S. Bankruptcy Court, District of Delaware, No. 11-13450.
(Reporting by Tom Hals in Wilmington, Delaware; Editing by Dale Hudson)