Bishop Joseph Toal, who was appointed Bishop of Motherwell on Tuesday, has raised "significant concerns" about the council's "commitment to provide Catholic schooling".
He promised to "stand together with the Catholic community" in opposing proposals in the local authority's recent consultation on school provision which would dramatically reduce the number of Catholic schools in the diocese.
Bishop Toal said in a letter to the council that proposals to alter the school estate provision have been "carefully considered, together with the consequences that these might have for the pupils, teachers, families and communities involved".
The Bishop said: "In the past few weeks the Diocese has met representatives from schools, parishes and the local communities and I have listened to their views on the matter."
The formal response from the Diocese of Motherwell then lists a series of "significant concerns about what some of these proposals might suggest about the council's commitment to provide Catholic schooling on an equitable basis within this Diocese."
The submission points out that at public meetings NLC officers claimed that larger secondary schools are necessary to ensure adequate curriculum provision. Yet, they are content to have non-denominational schools with rolls as small as 414 in one case and fewer than 700 in four other cases.
Across the authority, Catholic secondary school rolls would be on average one third larger than non-denominational schools.
This is highlighted by the Diocese, as "inequitable treatment of pupils attending Catholic schools."
In asking for a reconsideration of their proposals, the Bishop assures the council, "that the Diocese will always be keen to work in partnership with the Council to ensure the best provision of services to the community."
Councillor Jim Logue, Convener Learning and Leisure Services, said: "We are fully committed to both investing and supporting Roman Catholic education in North Lanarkshire.
"The new £19m school Our Lady of Good Aid Cathedral Primary School in Motherwell and £44million St Ambrose High School in Coatbridge alone demonstrates this commitment.
"Since 2006, the council has invested over half a billion pounds creating new schools and nurseries, including two new denominational secondary schools, nine denominational primary schools with eight of these on shared campuses. Within the shared campuses we have worked closely with the Catholic Church, schools and local communities to retain each school's unique identity and ethos while enjoying the benefits of the shared facilities.
"We have fully consulted with the Church on these and other school projects and we will continue to work together towards our shared goal of providing the best possible start in life for all our young people."