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.
"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.
Last year, 600 male teachers were dismissed and so far this year 550 teachers have lost their jobs for either kissing, touching or impregnating girls out a total teaching staff of 240,000 countrywide.
"A number of them have been taken to court, and they have been sentenced accordingly," Mr Hussein said.
Brian Weke, programme director for the Cradle, a child rights foundation in Kenya, agreed the problem was widespread.
He gave an example of a case in Nyanza province last year: "I found that in one primary school we had over 20 girls who were pregnant and nearly half the number were actually impregnated by the teachers themselves."
However, he said the officials investigating the abuse were not passing on vital information to get convictions.
"Our biggest problem is the fact that the district education officers - they do not report the matters to the police," Mr Weke told the BBC.
The BBC's Will Ross in the capital, Nairobi, says often teachers who are caught defiling their students end up paying the parents in order to prevent cases going to court.
Jane Thuo, a former teacher now with the Association of Media Women in Kenya, says female teachers are also starting to have illicit liaison with young boys.
"We see young men having affairs with older women and it is being replicated at school," she told the BBC.
Source: BBC News