Following the decision, Punjab, Balochistan and Khyber Pakhtunkhwa issued notifications on resumption of middle school classes from tomorrow.
However, Sindh Education Minister Saeed Ghani said schools in the province would reopen on Sept 28.
Earlier this month, millions of students in Pakistan returned to classes as educational institutions reopened after a break of six months.
In the first phase, all higher education institutions including universities, professional colleges, vocational institutes, as well as classes nine till 12 resumed on Sept 15.
Classes six to eight were scheduled to resume from Sept 23 in phase 2 while primary students were set to return to schools on Sept 30.
But tens of educational institutions were closed soon after across the country over violation of standard operating procedures (SOPs) and detection of Covid-19 cases among some students, teachers and other staff.
As a result, Sindh government announced a week's delay in implementing phase 2, with students of grades six to eight being asked to start schools on Sept 28.
Education minister Ghani said the decision was taken after he observed schools were not fully following coronavirus health guidelines.
Federal education minister Shafqat Mehmood had at the time said the government would evaluate the situation and announce a final decision on whether secondary schools will be opening as planned.
In a meeting today, the NCOC green lighted the second phase of reopening of schools from tomorrow as scheduled.