"My worry is those girls don't come back half of them pregnant," said Zainab Hawa Bangura told a luncheon at the British Residence in New York.
She was meeting with editors, Tina Brown and the British ambassador to the US in preparation for an unprecedented global summit next week in London on sexual violence in conflict. Angelina Jolie and British Foreign Secretary William Hague will co-chair.
The abduction of more than 300 schoolgirls by Boko Haram militants in April shocked the world and caused outrage among Nigerians. More than 200 girls remain captive.
And she told her audience that more than 2,000 girls in Nigeria already had been abducted before this case brought the situation to the world's attention.
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The fate of the schoolgirls is expected to be an intense discussion at next week's summit. Some aid and advocacy groups wonder how any pregnancies from rape in such a high-profile case will affect the wider debate over access to abortion services.
US foreign aid is prohibited by Congress from subsidizing abortions as a method of family planning, but advocacy groups have lobbied the Obama administration, including Secretary of State John Kerry, to issue an executive order saying aid could be used to provide abortions for women raped in conflict.