The public caning took place in the conservative state of Terengganu in the northeast of the country on Monday.
She said: "The public caning of the two women in Malaysia is a terrible reminder of the depth of discrimination LGBTI people face in the country and a sign that the new government condones the use of inhuman and degrading punishments, much like its predecessor".
Two Malaysian women convicted under Islamic law of attempting to have sex have been caned in public.
The pair, whose identities have not been revealed, pleaded guilty last month to breaking Islamic laws and were sentenced to six strokes of the cane each and a fine of 3,300 ringgit (26,000 baht).
Amnesty International said it was a "dreadful reminder of the depth of discrimination LGBT people face in the country and a sign that the new government condones the use of inhuman and degrading punishments, much like its predecessor".
Following widespread global criticism, a decision by the provincial Government earlier this year to ban public canings was met by strong opposition from local parliament, and religious activist groups.
They didn't cry or scream, they "showed remorse", Muslim Lawyers' Association Deputy President Abdul Rahim Sinwan told the AP.
"At a time when Malaysia would like to posture as a modern, civil and moderate government, this episode paints a black picture of this country", he said.
The case has not only prompted outrage among rights organizations, it has also cast a spotlight on what activists say is an increasing climate of hostility and discrimination against the LGBT community in Malaysia.
A member of the Terengganu state executive council, Satiful Bahri Mamat, defended the punishment, telling the agency it had not been meant to "torture or injure" and had been carried out in public to "serve as a lesson to society".
Authorities also removed the portraits of two LGBT activists from a public exhibition a few weeks ago, with the country's religious minister, Mujahid Yusuf, later saying that the government did not support the promotion of LGBT culture.
"Today is a dark day for human rights in Malaysia", he said, adding that such an inhumane act done in the name of religion would only bring shame to Muslims along with the entire nation.
Almost two-thirds of Malaysia's 31 million people are Muslims, who are governed by Islamic courts in family, marriage and personal matters. Homosexual activity is illegal under both secular and religious laws.
Malaysian Muslims have traditionally practised a tolerant brand of Islam but concerns have been growing in recent years that attitudes are becoming more conservative.