The mineral-rich island has witnessed an upsurge in fighting between the two groups following the collapse of a peace accord in August.
"Classes are not the same as before," said Amelia Abdul, one of 354 students at the Sambulawan Elementary School, about 60km north of Cotabato city in North Cotabato Province. "It's difficult to learn."
Her school - one of more than 200 - doubles as an evacuation centre for some 300 families trying to escape fighting between government forces and MILF rebels in the area.
In the back of the room the blankets and belongings of the people sheltering in the school - more than 1,500 people - are stacked along the wall.
According to local teachers, such conditions will have a serious impact on the area's children, many of whom could lose out on this year's education as result.
In Mindanao, the school year runs from June to March.
Scores of schools in the area, already badly affected by Typhoon Frank in June, have yet to resume normal classes.
More than 100 civilians have been killed in the fighting and scores more injured, the National Disaster Coordinating Council (NDCC), the chief government coordinating body for disaster and rehabilitation operations, reported on 29 October, with more than 2,000 homes damaged or destroyed.
Whole communities have been obliterated, say aid workers.
Of the 376,000 people receiving assistance, almost 100,000 are in evacuation centres in the area, many of them schools, with the rest staying with relatives and friends, the NDCC reported.
In Amelia's classroom, more than 100 children, comprising several classes merged into one, jostle for space as teachers struggle to keep control.
"It's very difficult to teach them. They can't concentrate with the chaos around them," said Norodin Alipoto, a grade-two teacher.
"We're not really using the lesson plan now because of the conflict," Kuyad Mascud, the principal, told IRIN. "And the students will suffer as a result."
Classes are being held more to keep pupils enrolled than actually teaching them anything, he conceded.
Thousands of children affected
While the total number of children affected is unknown, in Shariff Kabunsuan District, one of the worst affected areas, the impact is obvious.
According to Bai Alibai Aliuden, the division's school superintendent, some 9,000 students are not attending regular classes due to flooding as well as fighting.
Of the 200 schools in the district, 37 have been affected in recent months, with just six operating normally now, she said.
At the same time, one primary and one secondary school continue to be used as evacuation centres.
"Classes are not operating normally, with classes shortened to accommodate evacuees living at the centre," Aliuden confirmed.
Meanwhile, educators continue to hope for the best.
"It's been more than two months now. If the situation normalises, we will finally reopen classes. At this point, that's impossible," Mascud said.
"It's the children that will suffer most from this conflict," he said, hoping that the government and the 12,000 strong MILF would resume peace talks soon.