The official said the number of cases of sexual abuse was much more widespread than previously thought, adding that most of the cases are prevalent in the rural areas.
"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, the report added.
According to Brian Weke of Cradle Foundation, school officials do not usually report the matter to the police but he agreed the condition is widespread in the country.
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."
There were also reports that parents of these young girls were often given money to prevent them from reporting the cases of sexual abuse to the authorities.
It was likewise reported that female teachers are also having illicit affairs with their young male students. A former teacher, Jane Thuo said,
"We see young men having affairs with older women and it is being replicated at school," she told the BBC.