The Hump restaurant and two of its chefs, Kiyoshiro Yamamoto and Susumu Ueda, have been indicted on charges that could lead to long prison terms and hefty fines. Federal prosecutors say the chefs ordered the whale meat from fish importer Ginichi Ohira and served it at the restaurant.
Authorities say Ohira falsely described the product as fatty tuna on invoices and delivered to The Hump. Ohira pleaded guilty to a misdemeanor charge of illegally selling a marine mammal product.
Activists posing as customers were served whale meat on three occasions in 2009.
If convicted, Yamamoto faces up to 67 years in prison and Ueda faces a maximum of 10 years. The restaurant's parent company, Typhoon Restaurant Inc., would face fines totaling $1.2 million if found guilty.
Tests found the meat came from a Sei whale, an endangered species protected by international treaties.
Japan kills hundreds of whales in Antarctic waters each year under its research whaling program, which has triggered violent protests by conservationists and drew strong objections by diplomats.
Eating Sei whale meat is common in Japan, Korea and Norway and among native peoples in Alaska and Canada, but it is illegal to export the meat because of the Sei whale's endangered status.
The company and Yamamoto were initially charged three years ago, but prosecutors sought to have the charges dropped with the option to refile them at a later date.
The Associated Press contributed to this report.