The children, many of them reportedly orphans, were raced to hospital in the last two weeks in the northern state of Rajasthan after going into septic shock at the home outside the tourist city of Jaipur.
Three other children are fighting for their lives in a critical condition, according to the Hindustan Times newspaper on Sunday.
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Health and Family Welfare Minister J P Nadda said he dispatched a team to probe "the causes of water and food contamination" in a bid to "prevent such incidents in the future".
Nadda said 12 had died at the home for disabled people, with doctors and other officials saying last week that almost all of them were children.
"The five-member team will include a senior paediatrician, epidemiologist and microbiologist and will reach Jaipur today," Nadda said in Sunday's statement.
"A detailed report in the incident is expected shortly," he added.
According to the Hindustan Times, around 200 children, aged from six to 15, live at the Jamdoli government home, with about 10 to 15 sharing a bedroom each.
India has a poor history of treating people including children with mental disabilities and illnesses, and reports of overcrowding and shoddy care in institutions and homes are not uncommon.
For every one million people in India, there are only three psychiatrists and even fewer psychologists, according to the WHO.
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A doctor at the hospital in Jaipur, where some 15 children were initially admitted, said they were suffering from "septicaemia and septic shock".
"These were mentally handicapped and physically disabled children. The immunity of such children is usually lower than their normal, healthy counterparts. Their bodies find it tough to cope," medical superintendent Ashok Gupta told reporters last week.
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