Seventy-nine percent of the complaints were about tuition fee increases.
Another major complaint raised by parents was the refusal of schools to admit their children for various reasons such as lack of requirements or lost class cards, the DepEd said.
"We anticipated the public’s usual concerns about the first day of classes and, with the help our Oplan Balik Eskuwela partners, we were able to address them in advance," Education Secretary Florencio Abad said in a statement.
"Based on the calls we’ve been getting, we also recognize that there is much work to be done. We will continue to ensure that children are enrolled in school. Our efforts to solve problems, especially congested classrooms in overpopulated areas, are ongoing."
The public school system suffers from chronic shortages of classrooms, textbooks and teachers.
Several government agencies helped the DepEd prepare for the opening of school such as the Philippine National Police, the Metropolitan Manila Development Authority and the Department of Public Works and Highways.