Some Catholic schools are disbanding their Amnesty International support groups over its stance on abortion.
Amnesty said rape was used as a weapon in Darfur
The church's hierarchy in Northern Ireland said it was inappropriate for schools to support the organisation.
Amnesty International confirmed its controversial decision to back abortion in some circumstances, replacing its previous policy of neutrality.
The human rights group will campaign for women to have access to abortion in cases including rape and incest.
Several senior clergymen have resigned from Amnesty in protest.
The auxiliary bishop of Down and Connor, Donal McKeown, said a school in which he served as a governor had asked him if it should continue to have an Amnesty International support group.
"There was some concern about it already and I approached Bishop Walsh who, in response to that particular query from that particular school, said he thought it would be inappropriate, for an Amnesty branch to be continuing in the school.
"If it is a policy regarding one school, it certainly would be a policy regarding all the Catholic schools in the diocese of Down and Connor.
"Amnesty's espousal in recent months of campaigning for abortion access in limited circumstances will leave many people in a difficult situation.
"All we are saying here is that it seemed in appropriate in those circumstances for Catholic schools to be promoting the organisation."
Patrick Corrigan, Amnesty's Northern Ireland programme director, said: "Amnesty International and the Catholic church have more in common than that which divides us, namely the issue of sexual and reproductive rights."
Amnesty International said its position on abortion had been informed by its work in areas like Darfur, "where rape is used systematically as a weapon of war".
However, several Catholic schools in Belfast have stopped work for the organisation, including Rathmore Grammar and Our Lady and St Patrick's College.