Health CS Sicily Kariuki has ordered the ministry to probe the alleged death of 60 infants at Kiambu level Five Hospital.
The Kenya Medical Practitioners and Dentist Board (KMPDB) has also commenced investigations.
The findings of the inquest are expected to be released at the end of two weeks.
Of the 60 deaths, 30 newborns died in December 2018, another 20 died last in January.
Ten infants have already died at the hospital in the month of February alone.
Affected mothers and relatives raised the alarm but the hospital has defended its staff.
The hospital's medical superintendent Jesse Ngugi explained that the infants died because they were either born before their time or because they developed respiratory complications.
“The deaths can be explained because we do a mortality and morbidity audit for every death that happens in the newborn unit. That is to make sure we have continuous improvement in the quality of care we provide to patients,” Ngugi told journalists.
Joseph Mureithi told journalists that he has now lost two infants at the facility.
“I felt bad because it was my second child to die at the Kiambu Level 5 Hospital after being born. I don’t know why this is happening because the hospital is not explaining,” Mureithi lamented.
