Trinh Duy Trong, head of the department's politics and ideology department, said Monday most are primary school students.
Surveys at schools found that the parents of many of the children are factory workers, who were unable to care for their children when they were studying from home.
Covid-19 also forced many families to leave the city since they could not sustain themselves financially, the department said.
Khuu Manh Hung, head of the District 12 education department, said schools would cooperate with families to enable children to switch.
With the government deciding on a strategy of living with the pandemic, HCMC has resumed classes for students from seventh to 12th grades, but children younger than that are still at home, studying online.
As of mid-December around 2.2 million people across the country had abandoned cities to return to their hometowns due to Covid, 524,000 of them leaving HCMC.