Child, Youth and Family is transferring girls to secure youth justice facilities in Palmerston North and Christchurch, to make way for boys.
The policy change came to light after a 16 year-old girl spent four nights in police cells after Child Youth and Family failed to find her a bed in a youth justice facility.
Child, Youth and Family residential and high needs services general manager Nova Salomen said the decision was made earlier in the year, when there was an overflow of Auckland boys.
Ms Salomen says the boys were sent to Rotorua, Palmerston North and the South Island, while most of the girls resident at the time were from the middle and lower North Island.
She said at the time the decision made operational sense and she believed it still did.
Ms Salomen said the latest case was exceptional.
She said the girl was under the influence of a serious drug and was a danger to staff and police.
Ms Salomen could not say how many young people spent nights in police cells last month, but in June there were two and July there were six.
She said on average those children spent 1.7 nights in police cells.
Ms Salomen said while there are no beds for girls in the country's largest city, there are other options such as community providers and electronic bail.
The girl's lawyer, Jenny Verry, said the girl was held in a cell by herself but was distressed and unsettled as she heard adult prisoners screaming during the night. She said the teenager suffered from attention deficit hyperactivity disorder (ADHD). The teenager was facing 18 charges when she was taken into custody earlier this month.
Lawyer Jim Boyack was involved in the High Court trial of two boys accused of killing west Auckland dairy owner Arun Kumar.
He said a young person in police custody is held in isolation, and police cells do not have the facilities for holding people for long periods of time.
"For anybody to spend that amount of time in police cells without the amenities available in a remand youth justice facility for young people would in my opinion be tantamount to torture."
Ms Verry said the judge in the case was not impressed and had stated Child Youth and Family was not meeting its statutory obligations.
Two other girls, aged 15, were held in police cells for four nights in 2013.
At the time, deputy chief executive of Child Youth and Family criticised her staff's handling of the case, describing it as "too low, too slow".
The agency said as a result, a policy change meant cases involving young people in police cells would be referred to managers.