A three-judge panel at the U.S. Court of Appeals for the District of Columbia Circuit issued the decision Wednesday, the Miami Herald reported.
Last week, U.S. District Judge Royce Lamberth sided with detainees' attorneys, who said the search of their clients' genitals on their way to and from legal meetings were invasive and discouraged some of Guantanamo's 166 inmates from voluntarily leaving their cells for meetings with their attorneys.
"Doesn't the government have more important things to do than defend its right to grope detainees?" said attorney David Remes in Washington.
However, the groin searches were temporarily reinstated by the appeals court while the appeals court considers whether to overturn Lamberth's ruling.
The Justice Department has argued the searches were justified because guards have found "dangerous materials and other contraband" this year in cells at the prison.