A division bench headed by the Chief Justice Pradeep Nandrajog termed the matter "very serious".
The court had taken cognisance of a report published in a Hindi daily a few days ago, and ordered the Legal Services Authority (LSA) to conduct an enquiry therein.
An enquiry report was thereafter prepared by LSA and submitted to the court.
The Chief Justice and Justice Ramchandra Singh Jhala, while initiating suo moto cognisance on Thursday, directed Additional Advocate General SS Ladrecha to submit a status report, giving information as to what was the cause of deaths.
The district hospital of Banswara recorded the deaths of at least 90 new-borns in July and August. The state government has already ordered a probe into the matter.
The cause of deaths vary from birth asphyxia to low weight and pneumonia and infections, among other reasons.
Banswara district, which is mainly a tribal area, has a population of 20 lakh and has only one government hospital.