The ship had just offloaded a cargo of fuel and had left El Ade port - a site seized by Muslim fighters in fighting with an alliance of regional commanders last week that killed at least 70 people - when armed men stormed it on Wednesday.
"The ship was hijacked yesterday near Adale, 150km north of El Ade, after it dispensed oil," said Fuad Ali, who works with El Ade's port authoritiesl, said on Thursday.
"We have yet to find out details of the hijacking."
Somalia's lawless Indian Ocean waters are among the world's most dangerous.
Craft plying the waters often are attacked by armed men in heavily armed speedboats who demand ransom for the return of the ship or cargo, which often ends up being stolen.
The piracy has often stopped food aid getting into the poor country. Sailors have been held for as long as 100 days and a cruise ship with more than 300 on board was attacked with rockets and machine guns last year.
Somalia has no coast guard to protect vessels, but the US Navy earlier this month returned fire on a suspected pirate ship, killing one and wounding five while on patrol.
The country fell into anarchy after Mohamed Siad Barre, the last ruler, was ousted in 1991.