Some 20,363 children below 14 years gave birth in public hospitals last year after being defiled.
The youngest mothers were aged 10 years, according to data from the Ministry of Health.
This means some victims were impregnated as early as at age nine.
The figures, released by National Aids Control Council chair Angeline Siparo, show thousands of the children were also infected with HIV.
The crisis is worse for those aged 15 to 19 years.
"The same data showed us that for the girls aged 15-19, a total of 378,665 had been attended to in our health facilities as pregnant mothers," Siparo said in a statement on Wednesday.
Analysis of the data suggests most HIV positive children between 10-19 years were infected through sex rather than at birth.
"In 2019, the council noted with a sad note that a total of 6,247 children and adolescents aged 10 to 19 were newly-infected with HIV," Siparo said.
The Ministry of Health says deaths from HIV-complications in this age bracket are also growing.
In 2019, deaths among children and adolescents accounted for 21 per cent (4,333) and 11 per cent (2,275) of all Aids-related deaths respectively.
The ministry says this is alarming because the two groups are a small share of all people living with HIV in Kenya.
"Paediatrics and adolescents account for seven per cent (106,807) and six per cent (91,634) of all people living with HIV respectively," said Health CS Mutahi Kagwe on Tuesday during the World Aids Day in Kajiado.
Siparo said Nairobi has the highest number of girls aged 10 to 14 years impregnated last year, followed by Kajiado.
Siparo lamented the country continues to turn a blind eye to the crisis, yet there are laws to deal with it.
"Leaders across all sectors continue to remain enshrined and united in a culture of silence on the matter," she said.
The Sexual Offences Act provides that a person found guilty of defiling a child aged between 12 and 15 be jailed for not less than 20 years while whoever has sex with those between 16 and 18 years gets a minimum of 15 years.
The actual figures for 2019 are higher because the data captured only those who attended antenatal clinics.
Full figures for 2020 are not yet available, but health policy research group, African Institute for Development Policy, says at least 151,000 girls of 10 to 19 years were defiled and impregnated between January and May this year.
Afidep says it got its figures from the MOH-run Kenya Health Information Management System.
"From all the counties, the total numbers reported for the period January-May 2020 are 151,433 compared to 175,488 for the same period in 2019," Afidep said in June.
A decline in the use of health facilities during the Covid-19 lockdown and delay in the validation of the figures may account for lower numbers in 2020.
"KHIS data only captures cases reported in the health sector and so it is possible that there are many other pregnant girls who are not counted because they have not been to the health centres," the NGO said.