Hospital sources said 77 children died in December alone while 10 died on Monday and Tuesday.
Gehlot has given instructions to medical education secretary Vaibhav Galeria to visit Kota and submit a detailed report on an urgent basis.
"The chief minister has taken this issue very seriously and hence, I am here to find out the reason for neonatal deaths. A special committee will investigate if there were hygienic or clinical issues behind the death of these kids. Besides, all other issues will also be taken up," Galeria said after visiting Kota.
On being asked if there was a staff crisis hitting the hospital, he said: "A crisis has in fact been there, but I cannot comment upfront without complete investigation. We are trying to figure out the lacunae present here and also trying to find solutions."
Sources said that of 535 life-saving equipment, 320 were non-functional. Besides, only 27 out of 71 infant warmers were working. Some ventilators were also not working properly.
The hospital administration is, however, in denial mode.
Sources at the CMO confirmed that Gehlot is taking the case seriously and is himself monitoring the investigations.
Additional principal SMS college Dr. Amarjeet Mehta, senior paediatrician also visited Kota, along with Galeria.
Hospital sources said that all the children were brought in a critical condition to the hospital.
"Our investigation says that 10 deaths were normal and children did not die because of any negligence", said Dr H.L. Meena, hospital superintendent.
Similarly, head of the department (paediatrics) Amrit Lal Bairwa said, according to national Neonatal Intensive Care Unit records, 20 per cent deaths of infants are acceptable while 10-15 per cent deaths have been reported in Kota "which is not at all alarming".
The children were admitted in a serious condition, he added.
( With inputs from IANS )