Warfare is stopping 28 million children worldwide from receiving an education because of sexual violence and attacks on schools, the UN education fund says.
The report's author told the BBC one of the worst-affected places was the Democratic Republic of Congo, calling it "the rape capital of the world".
One third of the rapes reported in DR Congo involve children, Unesco says.
It also says to achieve the UN goal of education for all by 2015, Africa needs nearly two million new teachers.
"In the eastern part of the Democratic Republic of Congo probably about half of all primary school-aged children are out of school," Kevin Watkins, author of the report The hidden crisis, told the BBC's Network Africa programme.
He said the school attendance figures for Congolese girls were the lowest in sub-Saharan Africa.
"One of the reasons for that is that this has become one of the rape capitals of the world and is having a very profound effect on the education system."
The sexual violence harms victims' learning potential and creates a climate of fear that keeps girls at home, he said.
Military v education budgets
Militias tended to target symbols of authority when attacking a village, meaning schools and clinics were often destroyed, he added.
The Unesco report also details how in Afghanistan attacks on schools rose 77%, from 347 in 2008 to 2009 to 613.
And it says in northern Yemen 220 schools have been destroyed, damaged or looted during fighting in the past two years.
It calls on The International Criminal Court to take a far more active role in prosecuting those behind such acts of sexual violence and it wants an International Commission set up.
The under-funding of education is also highlighted.
The report names 21 of the world's poorest developing countries which spend more on military budgets than primary education.
Chad, for example, spends four times as much on arms as on primary schools.
It also highlights some advances like major increases in school enrolment in Africa.
Over a 10-year period Ethiopia reduced the number of people out of school by some four million.