A 23-year-old asylum seeker who was allegedly raped on Nauru has been flown to Australia for medical treatment, the Department of Immigration and Border Protection has told a Senate inquiry.

Fronting the Senate inquiry into serious allegations of assaults, and conditions at the detention centre, the department secretary, Michael Pezullo, said the Iranian woman was en route by air ambulance to Australia for medical care after advice was received by the International Health and Medical Services, the contracted provider of medical care at the processing centre.

The request from IHMS came through on Wednesday and was approved immediately, a department spokesman said.

The Greens senator Sarah Hanson-Young said her information was that doctors were concerned about kidney failure.

Nauru authorities have been investigating claims the woman was assaulted on a nearby main road when returning to the centre after visiting friends while on day release, despite initially denying she had been raped.

A submission to the Moss review accused the Nauruan police of a series of failures to investigate sexual assault. No one has been charged over the alleged assault.

The woman’s family has said she has self-harmed, has refused food and has been kept in a separate compound since the alleged attack.

Hanson-Young had previously accused the federal government of preventing the woman’s transfer, which the department has denied.

The Greens’ immigration spokeswoman said she was glad the transfer had now taken place, but “the fact that it’s taken three months to get her here is just unacceptable”.

She told the ABC on Friday morning the woman had waited 45 minutes after being found by police before being taken for medical care.

“The information that I was given at the time and has continued to be corroborated through evidence given to the parliamentary inquiry and through other sources, is that the police were watching the regular fireworks celebration while this poor young woman sat in the back of the police vehicle with nothing more than a blanket,” she told the AM program.

The Senate inquiry also questioned representatives from Wilson Security and a former guard who claimed asylum seekers had been waterboarded and cable-tied to beds.

The guard said he had not witnessed waterboarding but “what I firmly believe to be the actions after”.

Wilson Security denied those allegations, as well as others that the company had lied about the existence of a hotline for whistleblowers and drug and alcohol testing before July this year.

It also emerged that a fire during a 2013 disturbance at the centre had caused damage to the IT system, resulting in a six-month period with no central server, meaning records had been kept “ad hoc” by individual employees on their personal desktops.

At least one document – the “change of employment status” form for the senior Wilson Security guard who ordered the surveillance of Hanson-Young during her visit – was lost because of the interruption. The guard had been suspended on pay while the matter was investigated.

The Greens senator Scott Ludlam questioned what else went missing during that time, given Wilson Security had responded to various allegations by saying searches for evidence had turned up nothing.