A report by the Prisons Inspectorate found Wetherby YOI had improved on an already solid performance, but noted a series of concerns.
In addition to criticism of routine strip-searching, the loss of a prison-based social worker was said to have left an "unfilled gap", while conditions in the separation and care unit were judged unsatisfactory.
"All young people who were admitted and discharged from the establishment were still routinely strip-searched without a risk assessment and despite the introduction of a Boss (body orifice security scanner) chair and wand detector," the report said.
The concerns over strip-searching came despite a recommendation from a previous report that children and young people should only be strip-searched if a thorough risk assessment indicated it was is necessary to protect them or others from harm.
Last month, the Youth Justice Board (YJB) came under fire after it emerged a review of the controversial use of strip-searching in youth jails, initiated four-and-a-half years ago, has yet to be completed.
Concerns were also raised at Wetherby about the lack of a social worker and the fact the establishment did not have a record of the number of looked-after children they held.
Inspectors were pleased to find that the reception had been refurbished and early days continued to be well managed; self-harm prevention and anti-bullying arrangements had improved; managers were seeking ways to reduce the use of force; relationships between staff and young people continued to be very good; and mental health care was particularly impressive.
Nick Hardwick, chief inspector of prisons, said: "When we last visited, Wetherby was undergoing extensive and disruptive building work but was, nevertheless, performing reasonably well in all key areas. This inspection found that Wetherby had sustained, or improved on, this solid performance and, with the building work completed, was a more settled establishment."
Penelope Gibbs, director of the Prison Reform Trust's campaign to reduce child imprisonment, said Wetherby has made "great progress since the last inspection" and she was particularly pleased by the improvements in healthcare and the good relationships between staff and young people.
However, she said there were "a few things that really worry us". "The withdrawal of social workers across YOIs means there is little expertise in looked-after children or in child protection issues," she said.
"This report highlights a number of related issues. The use of force is still too high and restraint is used just to get boys to behave. And boys are routinely strip-searched on arriving and on leaving Wetherby, even though other ways of checking the boys are available."
