An internal review of the case is under way but changes have already been made.
A senior Immigration supervisor now has to approve decisions to detain someone in custody, which are then reviewed again after 24 hours and before the person is deported.
Staff who work with illegal migrants will also be given training on how to deal with victims of crime.
The Weekend Herald met with the family of the woman this week and no details which might identify her will be published.
No decision has been made on whether criminal charges will be laid following her complaint, but the police are still investigating the allegations of a serious crime.
Detective Inspector Colin Higson said the woman was provided with counselling and support following her complaint.
However, he said police were expected to tell Immigration New Zealand of people unlawfully in the country.
Higson declined to comment on the decision to deport her.
"The steps taken during an investigation are always on a case-by-case basis, and we work with partner agencies when required on what are often complex cases," Higson said.
"Any questions about the deportation of individuals from New Zealand should be directed to Immigration New Zealand."
Pete Devoy, the assistant general manager of Immigration NZ, said the organisation apologised "unreservedly" to the young woman and took full responsibility for the handling of her case.
"In the vast majority of cases our staff make the right decisions but in this case we accept that we got it wrong.
"As soon as senior managers became aware of the case INZ initiated steps to ensure the individual could return to New Zealand as soon as possible."
Devoy said the police asked about the immigration status of the woman, then asked for an update one month later.
That day, she was taken into custody under the Immigration Act for four days - then deported.
As in every deportation case, Devoy said the young woman was asked in an interview to state any "humanitarian circumstances" she wanted taken into consideration.
The decision to deport was approved by the immigration officer's manager.
However, Devoy said the manager was unaware of the criminal complaint laid by the woman and therefore her "status as a victim and witness".
"Immigration New Zealand accepts that it was inappropriate for her to be deported given the pending criminal complaint made by her and the related police investigation."
Her family laid a complaint with their local MP a week after she was deported and Immigration NZ became aware the next day.
She is now back in New Zealand.
"Immigration New Zealand has been in regular contact with the family throughout this process and has also met them in person to apologise for the distress caused and discuss the broader issues associated with the case," Devoy said.
The woman has been granted a six months' visitor visa so she has time to apply for the correct immigration status.