Another former inmate at the Marion C.M.U., Andy Stepanian, an animal rights activist, said a guard once told him he was “a balancer” — a non-Muslim placed in the unit to rebut claims of religious bias. Mr. Stepanian said the creation of the predominantly Muslim units could backfire, adding to the feeling that Islam is under attack.

“I think it’s a fair assessment that these men will leave with a more intensified belief that the U.S. is at war with Islam,” said Mr. Stepanian, 33, who now works for a Princeton publisher. “The place reeked of it,” he said, describing clashes over restrictions on prayer and some guards’ hostility to Islam.

Yet Mr. Stepanian also said he found the “family atmosphere” and camaraderie of inmates at the unit a welcome change from the threatening tone of his previous medium-security prison, where he said prisoners without a gang to protect them were “food for the sharks.” When he arrived at the C.M.U., he said, he found on his bed a pair of shower slippers and a bag of non-animal-based food that Muslim inmates had collected after hearing a vegan was joining the unit.

He was wary. “I thought they were trying to indoctrinate me,” he said. “They never tried.” The consensus of the inmates, he said, “was that 9/11 was not Islam.” “These guys were not lunatics,” he said. “They wanted to be back with their families.”