A spokesman for the church in Ireland confirmed that one of its grammar schools in Greater Belfast had been advised to wind up its Amnesty group. He also revealed that the Irish bishops will meet next month to discuss the presence of Amnesty in all Catholic schools.

Amnesty's policy that rape and incest victims should be entitled to abortions has led to calls from senior members of the Catholic church in Britain and Rome for a withdrawal of support from the organisation.

In relation to the banning of school Amnesty groups, a church spokesman told the Guardian: "An inquiry did come from a school principal, on behalf of the teacher who is in charge of the school Amnesty group, asking for guidance on the future of the Amnesty group in the school. The advice to the school is that it would be inappropriate for the school branch to continue in existence in the context of Amnesty International's new position regarding abortion."

Asked if the policy in Down and Connor, which includes all of Greater Belfast, would be extended, the spokesman said: "The sacredness and protection of all human life will be discussed at the next general meeting of the Irish Bishops' Conference."

Patrick Corrigan, Amnesty's Northern Ireland programme director, said he was still "hopeful" that the Amnesty school groups would not be affected by the row with the church hierarchy. "Amnesty International and the Catholic church have more in common than that which divides us, namely the issue of sexual and reproductive rights."

Across the Catholic world, relations between the human rights organisation and the church hierarchy have been severely strained over Amnesty's new pro-choice policy. One English cleric, the Catholic Bishop of East Anglia, Michael Evans, resigned from Amnesty after it took up a pro-abortion position. Bishop Evans, who was a founding member of Amnesty, said he regretted leaving it but had no choice as a Catholic.

Other Catholic bishops in Britain were more forthright in their condemnation of Amnesty's decision. The Scottish Catholic archbishop, Keith O'Brien, whose diocese is Edinburgh and St Andrews, said that in the light of the decision no Catholic should remain a member of Amnesty International.

Amnesty has said the issue of abortion arose over the mass rape of women in war zones such as Darfur and Congo.

The Vatican denounced the pro-choice policy, claiming Amnesty "has betrayed its mission". Globally, the Catholic church has withdrawn funding for Amnesty.