The girl, Oyetri Dey, had died at the AMRI Mukundapur unit last month.
Family members, including her mother, had alleged that she was not provided oxygen or given cardiopulmonary resus citation (CPR) on time after she had a convulsion following administration of an injection.
"Death was due to the effects of asphyxia as noted above ante-mortem in nature," the post mortem report, a copy of which is with the PTI, said.
A senior hospital official has denied the charges, saying the patient "had been on nebulisation and the oxygen mask was at her bedside. CPR was given promptly."
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The hospital had cited cardiac arrest as the cause of the death and said they suspected she had an underlying heart ailment.
Parts of the child's heart, lungs, liver, kidneys, brains along with the spleen, have been sent for histopathological tests.
The post-mortem report also stated, "Further opinion if any would be given after the receipt of the reports of preserved materials.
The commission heard the parents as well as the AMRI authorities.
Jayanti Chatterjee, the unit head of AMRI Mukundapur, who allegedly misbehaved with the girl's family, was also summoned along with and the doctor, Jayati Sengupta, who was treating the baby.
"We have asked both the parents and the hospital to submit affidavit stating their versions of what had happened," said Commission chairperson Justice Ashim Kumar Roy.
The next hearing would be held on Wednesday.