A teenage asylum seeker is being treated for undisclosed injuries in a Darwin hospital after jumping off a first-floor balcony at an unnamed detention facility last week.

The Immigration Department said the 16-year-old girl was now in a stable condition and had her mother with her.

The teenager had raised sexual assault allegations during her time in detention on Nauru, and those claims are now the subject of a departmental inquiry.

Immigration Department secretary Mike Pezzullo said he would show a personal interest in following up the case, which was considered "attempted self-harm".

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"I can give you an absolute assurance, we'll be particularly interested in the follow-up action once the girl's medical condition stabilises ... specialists [will] speak to her about her motivations, her feelings," Mr Pezzullo said.

"It's a pretty serious step to throw yourself from a height."

The girl had been transferred to Australia in January from detention in Nauru and could be transferred back there.

"You can be assured we won't be sending anyone on a long journey, such as to Nauru, if they're suffering any kind of consequences of falling from a great height," Mr Pezzullo said.

"I certainly as secretary will be taking a close interest in the follow-up to this matter."

The incident involving the teenager was discussed at a Senate estimates hearing in Canberra last night.

Immigration official Ken Douglas told the hearing the Immigration Department had received 44 reports of alleged sexual assaults which involved children or took place in detention facilities that housed children.

He said there had been 19 cases of reported sexual assault in detention on Nauru between July 1, 2013, and January 31, 2015, five of them involving children.

And he confirmed the teenage girl recovering in hospital had made allegations of sexual assault.

"I have seen a late report this afternoon to that effect, but I think ... the department is properly going to undertake further investigations into those claims," he said.

The author of the Forgotten Children Human Rights Commission report, Gillian Triggs, will appear before the Senate estimates inquiry again this morning.

Incident 'unsurprising', says advocacy group

An asylum seeker advocacy group repeated its call for all children to be removed from detention.

Peter Robson from the Darwin Asylum Seeker Support and Advocacy Network said the incident was not surprising.

"Unfortunately it's not the first time I've heard about this sort of self harm," Mr Robson said.

"The kind of conditions that young people are facing in detention centres at the moment leads to these things that are more common than not, unfortunately.

"So when I heard about it, I thought it was unsurprising."