Eight of the children lived in Belgium while the ninth was based in the Netherlands near the border with Belgium, said ministry spokesman Aad Meijer.
Earlier on Wednesday, Prime Minister Mark Rutte told Dutch news agency ANP he hoped all the victims would be quickly identified to put an end to the uncertainty, he added.
"For all those concerned, it is an unimaginable drama," said Rutte, speaking before the presence of Dutch children had been confirmed.
"In the first place for the children who were on the bus, and for their parents.
"Our thoughts are with them," he said, adding that he had sent heartfelt condolences to Belgian Prime Minister Elio Di Rupo.
The accident happened on Tuesday evening when one of three coaches taking the school party back to Belgium from a skiing holiday crashed into a concrete wall while travelling through a tunnel in southern Switzerland.
Another 24 children were reported injured in the crash, most of them with life-threatening injuries, said Jean-Pierre Dellars medical director of the emergency services in the region.