Family planning organisations caring for Kosovan rape victims are calling for the Vatican's status at the United Nations to be reviewed.
At the heart of the row is the supply of emergency contraception to refugee women who say they have been raped by Serbian troops.
The two sides in the debate discuss their differences on the Today programme
The Vatican has said that the issuing of the "morning-after pills" to Kosovan refugee women by international aid agencies is a form of abortion.
As a result, they want the Vatican's observer status at the UN looked into.
Offering emergency contraception to Kosovan women who have been raped is not an automatic response of aid agencies.
It is made accessible only as part of an overall programme of healthcare. Nonetheless, the IPPF says that the women are glad to have the choice.
Helping rape victims is part of a wider aid programme
"Women would at least like to be advised whether they have the possibility to prevent a pregnancy from developing. We know that these women are desperate to be advised about what they can do," said Ingar Brueggemann, Director-General of the IPPF.
The emergency contraceptive is only effective if taken within 72 hours of sexual intercourse. The Catholic Church has said that so soon after an attack a rape victim is too traumatised to make a decision.
"A woman in that condition has been violated physically, psychologically and emotionally. If you are in a state of emotional pandemonium, you are not in a position to be making a fair and informed consent," said Nicholas Coote of the Catholic Bishops' Conference in Britain.
Instead, he said, offering victims counselling and medical care was a more appropriate form of assistance.
The IPPF, and other aid organisations, feel that this is such an important issue that the status of the Vatican within the UN should be looked at.
"There is a movement to ask for the Vatican's position as a state within the UN to be reviewed. No one would deny that it should have a status as many of the other religious organisations have within the UN but as a non-governmental organisation," said Mrs Brueggemann.
The UN's debating chamber at its headquarters in New York
Holding observer status within the UN means that, although the Vatican can be present at UN meetings, it does not have the power to vote.
The Catholic Church has said that the aid agencies are looking to have this status reviewed, or removed, simply because they object to its stance on birth control.
The row comes as tensions build over family planning policy in the run up to a major UN conference next month.
The Vatican has encouraged developing nations to divert family planning aid budgets into general development aid budgets.
Donor nations like the UK oppose this move. World population will hit six billion this year and is projected to rise to nine billion.