Ms Mordaunt, who calmly listened to her, said she had been unaware of the concerns she raised, and offered to give up her second speaking slot at the end of the conference so she and her colleagues could address it.
Ms Pepper de Caires – who drew applause from the international audience at the Queen Elizabeth II Centre in London – was finally led from the stage by officials without further protest.
Ms Mordaunt said she was “very sorry” that some people had felt excluded from the event.
“The only thing I could do today to rectify that – because I think it is important that their voices are heard – is to give them a platform,” she told reporters.
“I personally didn’t know of their concern until today. We will do everything we can to ensure that people are able to speak up, they are able to articulate their concerns.”
She said that Save the Children had not received any government funding in relation to the new global register, being established by the Department for International Development and Interpol, announced earlier this week.
“It is not the case that Save are getting funding from us,” she said.