The 16-year-old boy alleges he was also deprived of exercise, adequate bedding and exposed to noise during his 28 days in custody in early 2023.
Watch houses in the stare are operated by the Queensland Police Service.
Children are allowed to be held in the facilities after the previous Labor state government in August 2023 overrode human rights laws with legislative amendments.
The government argued the move would ease pressure on youth detention centres, with two new facilities in the pipeline at Woodford and Cairns that will almost double capacity.
The boy was held in a watch house from January 6, 2023 on the day of his arrest until February 3, 2023.
The report found there were limitations of the rights to protection of a child and with concerns over privacy and humane treatment.
Allegations of such nature demonstrated watch houses did not meet the standards to safely accommodate children, the commission said.
Queensland Human Rights Commissioner Scott McDougall agrees.
"The allegations in this report are concerning and indicate a lack of protection, privacy and humane treatment for young people held in watch houses," he said.
"Lengthy periods of detention in watch houses, which are not designed or intended to hold children and indeed are only meant to hold adult detainees for limited amounts of time, will not result in rehabilitated children on release long-term."
Queensland police said the boy was given continuous support and his welfare and safety was paramount while he was in custody.
"Department and QPS staff are also provided with specialised human rights training to ensure that the human rights of those that are detained are at the forefront of their minds," a police spokesperson said.
The department of child safety said there were minimal releases from watch houses and detention centres over that period because courts were closed during the Christmas break.
That resulted in fewer beds at detention centres.
The commission said children should not be held in watch houses for longer than 24 hours.
It has made several recommendations to Queensland police and the department of child safety following the unresolved complaint.
The commission proposes developing minimum standards for children in custody, those rights being explained to kids and shortfalls to be met before complaints are lodged.
Queensland police is reviewing watch house operations.
Another review into failures of the state's child protection and working-with-children checks was announced by the LNP government in January.
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