The Church is pressing strongly for the Executive to retain a Christian dimension to school assemblies, presently enshrined in law, although many non-Catholic schools have quietly dropped traditional services because of their multi-faith and no-faith communities.
However, the Catholic Education Commission insists it is a matter of national significance.
John Oates, its field officer, said: "We would be very disappointed if the impact of Christianity on all schools was diminished. There are many Catholic pupils in non-denominational schools, particularly in rural areas.
"We feel that when we talk about inclusiveness that Christians should be included. Inclusiveness is often a concept that relates to small minorities but it affects everyone."
The commission believes schools will need help on developing the shared values they are being asked to celebrate through observance and assemblies.
It also denies that the creation of a national Catholic Education Service based in Glasgow is a response to the recent row about sectarianism and the Executive's support for legislation to outlaw it.
Mr Oates said the proposal for a national office had "been around for several years" but was only now coming to fruition with a new commission in place. Bishops approved the strategy more than a year ago.
A similar service with a full-time director already exists in London. The Scottish director, on a salary at least equivalent to the headteacher of a large secondary, is expected to be in post for the start of the new session in August. The director will establish the national office and will become "the public face of Catholic education".
Funding will come from the Catholic community, which is being asked to give generously during Catholic Education Week (February 16-23). Churchgoers will receive leaflets spelling out the benefits of Catholic schools.
Mr Oates, a former secondary head, will shadow the new director before bowing out.