Bishop Joseph Toal, who was appointed on Tuesday, said the Diocese of Motherwell has "significant concerns" over the council's schools proposals.
In a letter to the council, which accompanies a lengthy submission to the Chief Executive, the Bishop says the education department is not committed to providing Catholic and non-denominational schooling equally.
He said: "The Diocese has met representatives from schools, parishes and the local communities and I have listened to their views.
"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."
Bishop Toal's remarks come in response to the consultation on proposals to amalgamate Taylor High School and Our Lady's High School on a new campus with Bothwellpark ASL school.
The consultation will run until May 16 and a report on the outcome will be prepared and considered by councillors in September.
The proposed new £36 million joint campus would be based on the old Ravenscraig steelworks site.
In response, North Lanarkshire Council said it was "fully committed" to Roman Catholic education in the area, having built two new denominational secondary schools and nine denominational primary schools since 2006.
Councillor Jim Logue, Convener for Learning and Leisure Services at the local authority, said: "We are fully committed to both investing in and supporting Roman Catholic education in North Lanarkshire.
"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."