Immigration Minister Chris Bowen's confirmation on the ABC's Lateline program that children will not be spared from being sent to Malaysia under the asylum seeker swap is deeply disturbing, Amnesty International has said.

“Australia will be sending children into an extremely vulnerable situation – especially girls,” said Amnesty International Australia's refugee spokesman Dr Graham Thom.

“On top of the well-documented human rights abuses faced by all asylum seekers in Malaysia, unaccompanied women and girls face extraordinary levels of sexual violence and sexual harassment.”

There are currently 17 children on Christmas Island who have arrived since the deal was announced. Girls are among nine unaccompanied minors.

“With no family to protect them and no legal rights under Malaysian law, refugee women and girls will be at the mercy of gangs and officials who target them knowing they have nowhere to turn,” Graham Thom said.