A spokesman for the commission said March 3 that the body was shocked by the discovery made in Tuam, County Galway, at the site formerly managed by the Bon Secours religious order.
The Mother and Baby Homes Commission of Investigation is currently probing how unmarried mothers and their babies were treated between 1922 and 1998 at 18 state-regulated institutions, many of them run by religious orders.
Tuam Archbishop Michael Neary said during Mass March 5 he was "horrified and saddened to hear" the commission's revelations.
"This points to a time of great suffering and pain for the little ones and their mothers," the archbishop said.
"I can only begin to imagine the huge emotional wrench which the mothers suffered in giving up their babies for adoption or by witnessing their death. Some of these young vulnerable women may already have experienced rejection by their families. The pain and brokenness which they endured is beyond our capacity to understand. It is, then, simply too difficult to comprehend their helplessness and suffering as they watched their beloved child die," Archbishop Neary said.
The commission said the "remains involved a number of individuals with age-at-death ranges from approximately 35 fetal weeks to 2-3 years."
"Radiocarbon dating of the samples recovered suggest that the remains date from the time frame relevant to the operation of the Mother and Baby Home," it said.
The causes of death are, as yet, unknown. However, previous reports have highlighted the high levels of infant mortality in the homes due to disease and other natural causes.
The investigation will now center on why the remains were not buried in traditional graves and whether the deaths were reported to the civil authorities at the time.
"The commission is shocked by this discovery and is continuing its investigation into who was responsible for the disposal of human remains in this way," it added in a statement.
Katherine Zappone, Ireland's minister for children and youth affairs, said it was "very sad and disturbing news."
"It was not unexpected as there were claims about human remains on the site over the last number of years," she said. She added that everybody involved must respond sensitively and respectfully to the situation.
"Today is about remembering and respecting the dignity of the children who lived their short lives in this home," Zappone said. "We will honour their memory and make sure that we take the right actions now to treat their remains appropriately."