The 35,000-tonne MV Irene E M sent out a pre-dawn distress call but was rapidly taken, Alexandre Fernandes, a Nato Lieutenant Commander, said.
"There was only three minutes between the alarm and the hijack," Fernandes said.
"They attacked at night, which was very unusual. They were using the moonlight as it's still quite bright."
A Canadian warship has sent a helicopter to gain information as to the condition of the MV Irene E M.
"There are hostages so now we will shadow and monitor the situation," Fernandes said.
Shona Lowe, a UK-based Nato spokeswoman, confirmed the hijacking of the second vessel was unable to say how many crew may have been taken hostage.
She said that the pirates attacked from "three or four skiffs".
Also on Tuesday, the pirates launched a third attack, attempting to board the vessel while firing automatic rifles and rocket-propelled grenades.
The attacks follow eight other hijackings by pirates in the busy shipping lanes of the Gulf of Aden and Indian Ocean - known as the Horn of Africa - since the beginning of April.
Omar Abdirashid Ali Sharmarke, the Somali prime minister, told Al Jazeera: "We are gathering intelligence information on the activities, how these groups are working, what kind of connections and links they have and I think we are going to act soon.
"We are actually trying to do our best to try and disrupt the activities before we go to the waters," he said.
"The root cause was always the lack of institutions to deal with dissidents. You cannot just contain pirates from the seaside, you have actually I think to dissolve the bases from the land. You have to prevent them before they go into the waters."
Foreign navies patrol the area in an attempt to prevent the hijackings and in two recent raids they killed five pirates, rescuing a captured American captain and freeing a French yacht.
On Monday, the head of the group that seized the Maersk Alabama, from which the American was taken, vowed to retaliate for the deaths of his comrades.
The gangs, most of which are based in villages and small towns along Somalia's coast, demand multi-million dollar ransoms for the return of captured vessels.
Chris Davies, a commander from Nato's maritime command, told Al Jazeera that pirate attacks have increased but that operations against them might now be working.
Nato's fleet comprises of seven ships, including three with Nato's other alliances, in the Horn of Africa, an area of about 1.1 million square miles of ocean.
Three other coalitions, including the EU, have vessels in the area as well as individual nations, such as India and Japan.
"Without question there has been an increase [in attacks] in the last 12 months. There was a sharp rise in 2008 and that has continued into 2009," Davies said.
"[But] what we have seen is if there is a warship or one of the alliances in the area, you don't see the pirates."
Davies said that the gangs could now be changing their tactics launching attacks overnight due to the counter-operations.
"If they are doing that perhaps we are having an effect. They are not going out with impunity, they are trying to second guess where the ships are."
Analysts have said that until there is political stability in Somalia, where battles between the government and opposition fighters have precipitated a humanitarian crisis, it will be very difficult to prevent the armed gangs working offshore.