Commander John Harbour said he did not know the nationalities of the crew members onboard the St. Vincent and Grenadines-flagged Rak Afrikana.
Harbour said the ship appeared to be experiencing engine problems at the time it was hijacked early Sunday. EU forces have been dispatched to investigate.
International naval forces have stepped up their enforcement of the waters off East Africa in an effort to thwart a growing pirate trade.
Experts say piracy will continue to be a problem until an effective government is established on Somalia's lawless shores. The country has not had a functioning government for 19 years.