A report from an inquiry the government ordered in 2014 backed up a historian's claim that up to 800 children may lie in an unmarked grave at the home. It said: "significant quantities of human remains have been discovered in at least 17 of the 20 underground chambers which were examined".
Radiocarbon dating found the remains, which ranged from 35-week-old foetuses to three-year-olds, dated from between 1925 and 1961, when the home was run by the Bon Secours Sisters.
The inquiry was launched after a local historian said there was evidence of an unmarked graveyard at the home, where records showed almost 800 children died between 1925 and 1961.
The Church ran many of Ireland's social services in the 20th century, including mother-and-baby homes where tens of thousands of unmarried pregnant women, including rape victims, were sent to give birth.
Government records show that in the 1930s, 40s and 50s, the mortality rate for "illegitimate" children was often more than five times that of those born to married parents. On average, more than one in four children born out of wedlock died.
Ireland's Minister for Children and Youth Affairs Katherine Zappone said Friday's (Saturday NZ Time) news was "sad and disturbing", adding that the commission of inquiry would work with local authorities to investigate further and decide what should happen to the remains.
The commission did not say how many babies' remains were recovered or how many might still be buried in what are believed to be the home's sewage and/or waste water treatment system.
Ireland's once powerful Catholic Church has been rocked by a series of scandals over the abuse and neglect of children.
The Archbishop of Tuam said in 2014 he was horrified and saddened by the historian's discovery.