Prime Minister Abdullah Ahmad Badawi, who rarely singles out senior government officials for criticism, reprimanded Deputy Internal Security Minister Noh Omar late on Wednesday for apparently defending the police in the stripping of the unidentified woman.
A secretly shot video on a camera phone showed the naked woman, who appears to be Chinese, being made to perform squats in the presence of a policewoman.
"I reprimanded (Noh) on the matter," Abdullah told the national news agency, Bernama.
"Government officials should be more sensitive and careful when issuing statements on the issue."
Noh had insisted Tuesday he believed police had not flouted procedure in making the woman strip.
"If foreigners feel we are cruel, they don't have to live in Malaysia, they can go back to their own countries," Noh told reporters.
He later claimed his remark was misinterpreted and apologised for any ill feeling it sparked.
Abdullah told Bernama that Noh's comments did not reflect those of the government, and that Malaysia welcomed tourists and other foreign visitors.
The nude video has bolstered claims by human rights activists that police routinely mistreat detainees, and also raised concerns that the Malay-dominated police unfairly target Chinese, whether foreigner or local.
Ethnic Chinese comprise about a quarter of Malaysia's 25 million people, while the majority are ethnic Malays.
Police have not yet traced the woman in the video, which was filmed by an unknown person.
The video footage was delivered anonymously to opposition lawmaker Teresa Kok, who went public with it last week.