Most cases of abuse reported have occurred in rural schools.
More than 1,000 teachers have been sacked in Kenya for sexually abusing girls over the past two years, the authorities say.
Senior government official Ahmed Hussein told the BBC that most of the victims were aged between 12 and 15.
He said a nationwide confidential helpline set up to help victims had revealed that the problem was much more widespread than previously thought.
Most of the cases have occurred in rural primary schools.
We had over 20 girls who were pregnant and nearly half the number were actually impregnated by the teachers themselves”
Fear of rape 'traps Kenya women'
"Initially we were not able to know what was happening in the country because of the poor communication, but now communication is everywhere - there's mobiles across the country," Mr Hussein, from the Ministry of Gender, Children and Social Development, told the BBC's Network Africa programme.