The children who died were between six months to two years old, officials said.
Two toddlers died and 10 children were hospitalised after they allegedly consumed contaminated food, earlier this week, at an orphanage in Mathura, a senior district official said.
District Magistrate, Sarvagya Ram Mishra, on Thursday said: "It is very very unfortunate that 12 kids took ill due to food poisoning out of which two lost their lives. The children who died were between six months to two years old.
"Six children were referred from here to Agra. It is from those six that the two casualties have occurred, the six others here are recovering as per the doctors," Mr Mishra said.
He added that the cause behind the death of the innocent children seemed to be "food poisoning" and added that had the authorities been diligent the casualties could have been averted.
"Prima facia, it seems to be a case of food poisoning, these are very small kids so proper care should have been taken, and higher authorities should have been alerted quickly. Some negligence by the staff too has happened. The matter should have been brought to our notice immediately," he said.
"The matter which has been brought to our notice today should have been brought to our notice the day before. We will ensure the guilty people are dealt with strictly after proper investigation within 24 hours," he added.