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Ms Zappone's letter was included in the collection of publicly available submissions to An Coimisiún Pleanála obtained by the Special Advocate’s office.
Two weeks ago, An Coimisiún Pleanála upheld planning permission for a 106-apartment development on the former Bessborough Mother and Baby Home site in Cork.
In correspondence, Ms Zappone, who as minister for children held responsibility for the oversight of the Mother and Baby Home Commission (2016-2020), made a number of observations, including that "enough was not done to determine burial sites" at Bessborough.
The submission dated 13 April states that "there were modest efforts to do so (locate burial grounds) at Bessborough by the Mother and Baby Home Commission, but these were not sufficient or similar to the efforts made at Tuam".
The former minister also rejected the planning requirement to have forensic archaeologists on site during building.
"It seems logical to conclude that builders who are working on the site would hold even greater potential to destroy human remains, even with monitoring, thus potentially obliterating any kind of possibility of DNA identification," she said.
Ms Zappone suggested that An Coimisiún Pleanála seek information from the lead forensic archaeologist as to why the Mother and Baby Homes Commission of Investigation did not ask them to conduct a Ground Penetrating Radar examination of the grounds.
She stated in the letter that in respect of Bessborough, "the Mother and Baby Homes Commission of Investigation did not request [lead consultant Forensic Archaeologist] (who was their consultant to them on these matters) to do the same kind of initial testing for potential human remains as was done in Tuam".
"No Ground Penetrating Radar was used (in Bessborough) as it was in the first phase of testing in Tuam," she said.
She emphasised that it was her direction while minister, that the Institutional Burials Act 2022 "should also apply to all other potential burial sites at the various mother and baby institutions".
The Special Advocate for Survivors has said the letter of objection by a former minister who held responsibility for the Mother and Baby Homes Commission of Investigation "clearly indicates that the former minister is concerned about the sufficient efforts by the commission to locate infant and child remains in Bessborough".
Patricia Carey said many mothers and other family members had contacted her requesting that she raise the issue of their not knowing where their child is buried on the grounds of institutions across Ireland.
"The fact that there is no definite identification in these burial grounds is a heartbreaking situation for those mothers and the wider family members of those children who died," she said.
Ms Carey has urged the State to reinvestigate to ensure the burial grounds can be finally and comprehensively identified.
She said Section 8 of the Institutional Burials Act relating to 'Burial Grounds Regulations' allows for further, forensic and final identification of burial grounds.
The Special Advocate has also reiterated her request for the release of sealed Mother and Baby Homes Commission of Investigation records, documentation and reports relating to burial ground investigations in all institutions.
This she said would indicate the State's "commitment to transparency", in response to concerns expressed by survivors and their families that the Commission of Investigation had not fully investigated potential burial sites.
"Burial investigations are not 'witness evidence', therefore I see no bar to their publication.
"Under section 11(3) COIA 2004 a court can direct disclosure of evidence and records contained in the MBHCOI Archive. I am calling on the Taoiseach and the Minister for Disability, Children, Equality to instruct the Attorney General to seek such a court order immediately," she said.
The Special Advocate has joined others in calling for a Compulsory Purchase Order by Cork City Council of the Bessborough site; as well as further investigation of the Bessborough grounds, including through non-invasive archaeological methods, to identify the burial grounds of 859 babies, infants and 19 mothers who remain disappeared.
The Special Advocate has called for engagement by the State with Survivors and Affected Persons of Bessborough, and the Special Advocate for Survivors, to determine a shared approach to memorialisation and dignified burial for the 923 infants and children, as well as the mothers who died at Bessborough.