Joseph Toal, appointed Bishop of Motherwell on Tuesday, raised concern about North Lanarkshire Council's plans to close two secondary schools.
The authority is consulting on the merger of Our Lady's High and Taylor High in Motherwell with plans for a new £36 million school at Ravenscraig, on the outskirts of the town.
The council believes the proposal is necessary because of deteriorating buildings at both Catholic schools - with the former steelworks site at Ravenscraig ideal for a large new school.
However, parents and local politicians have opposed the plan, arguing the existing schools are in a reasonable condition and are vital to their communities.
In a letter to the council, Bishop Toal said the diocese has met representatives from schools, parishes and the local communities involved.
The Diocese of Motherwell listed 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".
In particular, the diocese said council officials had argued larger schools were necessary to ensure adequate curriculum provision.
It added: "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."
The diocese claimed this was "inequitable treatment of pupils attending Catholic schools".
In asking for a reconsideration of their proposals, the bishop assured the council the diocese "will always be keen to work in partnership with the council to ensure the best provision of services to the community".
However, Jim Logue, the council's convener of learning, dismissed the suggestion Catholic education was being poorly served.
He said: "Since 2006, the council has invested over half-a-billion pounds creating new schools and nurseries, including two new denominational secondary schools and 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."
Parents have accused the council of trying to use the development - which also involves Bothwellpark High - as a way of generating more interest in the Ravenscraig redevelopment among housing developers and major retailers.
The council has been at pains to state that, following detailed assessments, the site is ready to use and there are no post-industrial health and safety risks.