The freighter had offloaded 400 tonnes of the total 850-tonne cargo of food aid in the port of Merka, about 100km south of Mogadishu, when six armed men stormed the ship and forced it to leave the port, the World Food Programme said in a statement.
Andrew Mwangura of the Seafarers' Assistance Programme told journalists the ship's captain called the Kenyan port city of Mombasa and reported the hijack.
The ship, the St Vincent and Grenadines-registered MV Miltzow, which was seized at about 3.30pm (1230 GMT), is the second WFP-chartered ship to be hijacked in Somalia waters.
On 27 June, unidentified pirates seized control of MV Semlow as it was ferrying 850 tonnes of German and Japanese donated rice to tsunami victims in northeastern Somalia, but the vessel was abandoned last week in the port of El-Maan after WFP and ship's owners refused ransom demands.
"It is scandalous that a small number of profiteers would once again hijack humanitarian food supplies destined for fellow Somalis," WFP country director for Somalia, Robert Hauser, said in a statement.
Somalia has been without a
government since 1991
"The cargo - consisting of 703 tonnes of maize, 108 tonnes of beans and 39 tonnes of vegetable oil - was destined for the Lower Juba Valley, which is home to some of the most vulnerable people in Somalia, people who have repeatedly been affected by droughts and floods," he added.
The latest hijacked vessel had 10 crew members - a Kenyan captain, a Ugandan engineer and eight Kenyan crew members.
In Nairobi, government spokesman Alfred Mutua advised Kenyans against sailing to the Somalia coastline "because of the high incidents of piracy and kidnapping... to which many Kenyans have fallen victims".
Moments after Wednesday's seizure, Yusuf Indha Adde, the governor of the Lower Shabelle region, immediately sent two boats to pursue the vessel but there were no reports of the outcome, according to WFP.
MV Miltzow became the fourth vessel to be seized in the pirate-infested Somali waters amid a flurry of new piracy warnings for the area. Somalia itself, a nation of up to 10 million people, has lacked a government since Mohamed Siad Barre was toppled in 1991.
"It is scandalous that a small number of profiteers would once again hijack humanitarian food supplies destined for fellow Somalis"
Country Director - Somalia,
World Food Programme
On 24 September, the same pirates took control of a ship transporting cement from Egypt, and last week another ship, MV Torgelow, was seized as it sailed with supplies for MV Semlow, which had run out of fuel.
The tsunami food aid is still in MV Semlow, currently docked in El-Maan, where port authorities have failed to cooperate for the rice to be offloaded and distributed in central Somalia, the WFP said.
In most of the hijacked ships, armed men had demanded hefty ransom in exchange for the return of the vessel and crew.
Last month, the US State Department renewed its regional terrorism alert for East Africa, noting in particular increasingly violent attempts by Somali pirates to seize commercial ships.
In an alert released this month, the International Maritime Bureau said at least 22 attacks had been recorded off the Somali coast since 15 March and urged ships in the area to stay as far as possible from shore and keep to the minimum the use of radio communication, including VHF.