The Commissioner of Correctional Services, Lam Kwok-leung, said on Sunday that it has never been a requirement for new prison inmates to strip naked and squat and then answer questions from guards.
Lam was referring to a claim by pro-democracy activist Joshua Wong, who says he underwent such an experience when he was jailed in August.
Wong said in an interview that the three-minute ordeal left him feeling humiliated.
Lam said the activist should have made a complaint at the time, adding that he didn't know whether Wong had actually done so.
Wong is currently on bail while waiting for an appeal against his prison term over a protest in 2014 which sparked the 79-day Occupy sit-ins.
He responded to Lam's comment by saying the official was either not telling the truth or he was unaware of the actual situation in the SAR's prisons.