According to the officials, only 20 per cent students were in attendance on an average.
An education department official attributed the low attendance rate to violence-related issues, transportation and fear among parents and children.
Meanwhile, 96 schools have remaned closed as relief camps for the displaced people have been set up in the premises.
Of these, the highest number of schools at 41 are in Churachandpur district, followed by 17 in Bishnupur; 10 in Kakching; eight each in Kangpokpi and Imphal East; four each in Ukhrul and Tengnoupal; and two each in Imphal West and Thoubal.
Chief Minister N. Biren Singh said that classes 9-12 will resume once the construction of pre-fabricated houses for the displaced people are completed.
The Manipur government had earlier decided to reopen the schools on June 21 and July 1, but it could not.
Over 50,000 people of different communities are taking shelter in over 350 relief camps across the state after the ethnic violence broke out.
The conflict has so far killed some 150 people and injured over 500 others, while aa large number of properties, including houses, shops, vehicles have also been destroyed.
IANS