"Children are coming back to the Vladimir Nazor Primary School in Pribislavec," Vican said on Thursday afternoon, adding that the ministry would continue monitoring the situation in the school.
Vican said that parents had shown understanding and were willing to look at the problem from various aspects.
A representative of the dissatisfied parents, Gordana Barila, said that Education Ministry officials had demonstrated readiness to tackle the problems in the school.
"Some problems will be solved immediately, and some in the long run," she said.
About 160 pupils of the primary school and their parents started boycotting classes on Tuesday by protesting in front of the school because of what they said was the systematic and years-long physical and mental harassment of the children by several Roma pupils.
After a failed meeting with the school's principal last Friday, the parents opted for a boycott until their demands were met.
The Pribislavec Primary School is being attended by 350 pupils.