Geoffrey Shannon's report examines the use by Gardaí of Section 12 powers under the Child Care Act 1991. Section 12 powers are emergency measures that Gardaí can use to remove children from their families or guardians if the children are deemed to be at serious and immediate risk.
In response to the report, a spokesperson for Tusla said: "An Garda Síochána is a crucial partner in the area of child protection and both agencies have distinct functions, powers, responsibilities and methods of working.
"Much of the research for this audit was done over the past number of years and collaboration and services have significantly improved since that time.
"This report was commissioned for An Garda Síochána, and Tusla was not involved in its production. No Tusla staff were interviewed as part of this audit."
Dr Shannon said he was distressed by Tusla's response which, he said, created the impression he had not afforded the agency due process.
Dr Shannon said he "felt compelled to address the issue".
He said he had "ongoing contact with Tusla throughout the whole process and that he always affords due process".
He also challenged Tusla's claim that his report was based on historical data, saying his report is "a contemporary picture of the child care system in Ireland".
Tusla later issued a statement, which said the agency was contacted by Dr Shannon and did engage with him.
It added: "However the report was commissioned by an Garda Síochána and in line with this Tusla was not specifically involved in the final report. No Tusla staff member was interviewed for the process"
This afternoon, Tusla Chief Operations Officer Jim Gibson said that child protection is everybody's business and the agency is on a road of "reform and service improvement".
He said these improvements include improving the agency's out-of-hours service and the development of an IT database listing all at-risk children.
He said 1,295 children are listed on that database which hospitals and gardaí have access to.
Speaking on RTÉ's News At One, Mr Gibson said there were also emergency placements across Ireland.
In 2015, he said, Tusla's emergency out-of-hours service received 369 referrals, and out of this number, 280 children were placed in alternative care.
He added that, to his knowledge, none of these children were brought to a garda station.
Mr Gibson said that as austerity is coming to an end, there is investment in services which will allow the pressure to be removed from crisis points.
Children's Ombudsman Niall Muldoon earlier said the report is "very concerning".
Speaking on RTÉ's Morning Ireland, he said that he has not seen the report yet but it appeared that many areas of concern, such as inter-agency cooperation, remain problematic.
Dr Muldoon said there was a clear need for a co-location of child protection services.
He said 24/7 services that should be in place are not available and it is draconian to remove children from their homes and bring them to garda stations.
Dr Muldoon added that all gardaí should have special training in dealing with children.
When asked if Tusla was fit for purpose, Dr Muldoon declined to comment but said its ability to self correct "seems to be slow" and this must be addressed.
Children's rights expert and former senator, Jillian van Turnhout has said the lack of communication between gardaí and Tusla is extremely worrying and should ring alarm bells.
Speaking on RTÉ's Drivetime, she said mechanisms need to be found to ensure there is much better oversight.
Ms van Turnhout said the blame lies with both An Garda Síochána and Tusla, adding that agencies need to be working together to protect children.
"If we look at the report and see how children are taken into care (by gardaí), the problem is they then cannot access the services and care that they need.
"If a child is deemed to be returned to their family by Tusla the guards are not told the reason for that happening and are not involved in that decision making process.
"They need to involve the guards in understanding those decisions because if the guards don't agree, they have no avenue in which to appeal that decision."
Meanwhile. the co-director of Pavee Point has said today's report on the child protection system highlights the need for a 24 hour service to uphold child protection of the State.
Speaking on RTÉ's Drivetime, Martin Collins said the report's findings show serious and shocking failings in Ireland's child protection system.
He said his organisation is particularly concerned that the State is still not implementing an ethnic identifier in order to monitor the equality of services.
