Peter Martens, also from the crisis management centre, said the Belgian authorities were trying to establish contact with the ship through diplomatic and military contacts and that they would "find out more in the coming hours hopefully".
Alexandre Fernandez, a Nato conmmander travelling with a fleet patrolling the Gulf of Aden, told Al Jazeera that the ship was hijacked at night.
"We know that the ship has 10 crew members - two Belgians, one Dutch, three Filipinos and four Croatians," he said.
The 1,850-tonne Pompei, belonging to the Jan de Nul group, has accommodation for 19 people.
It is used for installation of rock protection on offshore pipelines or for underwater rockberm construction, according to the company website.
Earlier, the Dutch navy embarked on a rescue operation that freed 20 Yemenis who had been held for more than a week.
Seven pirates, who surrendered without exchanging fire, were captured but were later freed by the navy for legal reasons.
Fernandes said that Nato did not have jurisdiction to prosecute pirates.