ODT inquiries revealed Child, Youth and Family using motel rooms to hold children in remand under the watch of security guards because of a lack of beds.
Child, Youth and Family Southern regional director Theresa Perham confirmed the practice, but said the department did not "believe there have been any situations this year when Otago Youth Justice have used a motel in these circumstances".
"There will be some circumstances where a placement capable of detaining a young person is not immediately available," Mrs Perham said.
"To avoid a young person being returned to police cells overnight while waiting for a placement for their safe detention, we have occasionally used motel rooms.
"In some cases that assessment will lead us to obtain the use of a security guard to support our staff. Security guards are not placed in a position where they are alone caring for children or young people, and nor are they expected to physically restrain or detain children or young people. If a situation does escalate, security guards and our staff are expected to phone the police.
"The use of motels is a place of last resort."
The ODT was also informed CYF's Will St, Abbotsford, residence, which was not operating at present, had also been used to house children remanded into CYF custody.
CYF first responded to the claims by saying "it has only been used for care and protection cases, not youth justice", but, following further inquiries, it was conceded: "One young person was placed at Will St on 19 October, 2016, after being remanded into CYF custody by the Dunedin Youth Court."
"The young person stayed for one night and was accompanied by two CYF staff members," Mrs Perham said.
"The following day, they were transferred to a Youth Justice residence."
Dunedin youth advocate Brian Kilkelly said he was not surprised by the low numbers reported as spending more than 24 hours in police cells because of the stance adopted by local Youth Court judges.
"I would accept those figures that the ministry is giving at the moment," he said.
"But that reflects the very conscious effort that local Youth Court judges have made that a prison cell isn't a place for a child and they are saying without debate 'I'm remanding these children into the custody of the chief executive of the department'."
Mr Kilkelly has voiced concerns about Will St sitting idle and the effect that has had on youth offenders being remanded into police cells or to Youth Justice residences far from home.
Despite claims from the Ministry of Social Development that there were no guarantees the Will St house would be appropriate for youth offenders on remand even if it was operating, Mr Kilkelly said it had been used in that fashion for years while in operation.
The issue of a lack of appropriate beds for youth offenders even prompted the Principal Youth Court Judge to tell the Otago Daily Times police cells were "no place for vulnerable young people and children".
"Youth Court judges in some parts of the country are reporting that an ongoing shortage of places in CYF residences for young people who cannot be released on bail has meant more children are being held in police cells," Judge John Walker said.
"Although the law allows for young people to be remanded in police cells when there are no CYF beds available, cells are no place for vulnerable young people and children, no matter how short a stay.
"Some of these teens are as young as 14; they may have mental health issues or neuro-disabilities. A high proportion will be subject to the care and protection jurisdiction of the Family Court. Yet because they need to be kept separate from adults in police custody, they are effectively held in solitary confinement."Police do what they can, but they cannot make adult cell blocks appropriate for young people."
A Ministry for Social Development spokesman said it was not CYF's "first choice to have a young person remain in cells pending a Youth Court appearance, but we have to strongly consider the safety of both the young person and the community at large".