The Department of Education wants the Edmund Rice Schools Trust to relinquish control of the building.
School patron Archbishop Diarmuid Martin and the board of management have already agreed to the plan.
But RTÉ News has learned that the trust has raised legal obligations, which it says could prevent it from releasing the property at less than its commercial value.
The Archdiocese of Dublin agreed to merge two small Catholic primary schools (a boys' school and a girls' school) into one building on Basin Lane.
Both schools have seen falls in enrolment over recent years.
The amalgamation was intended to free-up a Christian Brothers building to house an Educate Together school.
It was hoped the new multidenominational school would open its doors in September.
However, sources close to the trust, told RTÉ News that the trust is constrained by its charter, which obliges it to use its assets for the benefit of Catholic education in the spirit of Edmund Rice.
This may mean that it cannot give away property at less than its commercial value.
In an email statement to RTÉ, it said it owns the property and has agreed to a merger with the nearby Mater Dei Primary school from next September.
It said it was now in discussions with several bodies who had expressed an interest in the property.
They include the Department of Education and other local community groups.
It said the issue was how the property could now be best used to serve the local community in the Basin Lane/James Street area.
The Department of Education said that discussions are ongoing and it hopes the new school will open this year.
In submissions to the Forum on Patronage and Pluralism, which reported last year, the Catholic bishops raised what they called complex legal issues surrounding the transfer of properties. They said communities were likely to expect compensation.
In a separate submission, the trustees of Catholic schools warned that trusts might require financial recompense for any transfer.
The Edmund Rice Schools Trust was established over five years ago by the Christian Brothers.
The congregations transferred control of its schools and school properties to the trust.
The Christian Brothers congregation continues to owe the State millions of euro in compensation related to institutional abuse.
These negotiations relate to one school, but could have implications for the transfer of Catholic school buildings across the country to other forms of patronage.
The Department is currently surveying parents in 38 areas around the country in a process that could lead to the divesting of some Catholic schools to other multi-denominational forms of patronage.
Friday was the closing date for completion of the surveys.
The Department has already completed surveys in five areas and found immediate demand for a new multidenominational school in each area.