The latest move comes after the Scottish Executive refused to intervene to block North Lanarkshire's plans for shared facilities in seven new primary campuses to be built under a public private partnership (PPP) programme.
A statement issued by Bishop Joseph Devine of Motherwell, chairman of the Catholic Education Commission, said the Church would now take legal advice on a judicial review to halt the plans.
The Church is demanding separate entrances and reception areas, separate staffrooms, separate libraries and wants to stop pupils crossing on their way to use shared facilities. The council says this would be too costly.
Bishop Devine took his protest to the First Minister on the grounds that these proposals would lead to a "significant deterioration" in the provision of denominational schooling in North Lanarkshire, and were therefore contrary to section 22D of the 1980 Education (Scotland) Act.
In a detailed seven-page reply on behalf of ministers, Philip Rycroft, head of the schools group in the Executive's education department, comprehensively rejects this argument and insists that ministers' consent to the North Lanarkshire proposals is not required.
Mr Rycroft's letter states: "Ministers noted that the hierarchy's representations make no mention of any significant deterioration in the comparative 'distribution or availability' of school education.
"The council's submission (states) that, because the seven proposals involve no closure of denominational schools, or transfer of pupils to another denominational school, or changes to current catchment areas, or changes of site beyond the very local, or pupils having to travel distances that would necessitate the authority to provide transport, the distribution and availability of school education in denominational schools as compared with non-denominational schools will remain essentially the same."
His letter also considered whether the "provision" of Catholic education in North Lanarkshire was likely to deteriorate under the plans, in particular the distinctiveness of Catholic education and the ethos of the Church's schools. The hierarchy argued that the requirement to "secularise" shared areas would significantly diminish these elements.
The Executive begs to differ. "Ministers consider that section 22D is concerned with maintaining the pattern and balance of denominational and non-denominational education," the letter states. "They consider that, if these proposals are implemented, the pattern and balance will be maintained in North Lanarkshire."
There was no evidence from any of the shared campuses in Scotland that they had resulted in "significant deterioration" for pupils of denominational schools.
Mr Rycroft concluded that the shared campuses would not impact disproportionately on one school. The Executive suggests the council can be relied on to encourage headteachers to manage shared facilities appropriately.
The Church's statement said no further comment would be made until it had considered legal advice.