Speaking at a news conference, Du Four said: "We have three people dead and 10 in various hospitals."
He did not immediately identify the suspect, who was injured as police detained him and taken to a nearby hospital.
The VRT television network said the man was local and known to police.
Speaking to Al Jazeera, Teri Schultz, a freelance journalist in Dendermonde, said people in the small town were shocked by the incident.
She said: "There are some very seriously wounded children still in hospital. It is a bizarre and tragic story.
"The man, with his face painted black and white,... arrived on bicycle at the centre, knocked on the door and started stabbing these children, many of whom were in their beds taking a nap.
"Childcare workers tried to place themselves between the children and the attacker, and one of those female workers was killed on the scene, as was one of the children, another child later died in hospital," she said.
"He walked back out of the building, got back on his bike, rode off and was apprehended by police."
Du Four said police showed photographs of the youngsters who had been taken to the hospital to parents, asking them to identify their children.
The city used a nearby community centre to provide counselling to victims and witnesses of the stabbings.
Shultz said: "A woman at the childcare centre said there is no known connection between the attacker and the centre, and no known connection between the attacker and any of the children or the adults.
"They have absolutely no known motivation for the attack."
Veerle Heeren, the social welfare minister for the regional Flemish government, said she would be investigating security measures at the creche.