It was the first conviction for same-sex relations and the first time a caning had been carried out in public in the state, Reuters quoted Satiful Bahri Mamat, a member of the Terengganu state executive council, as saying.
The women, aged 22 and 32, were arrested in April by Islamic enforcement officers after they were found in a vehicle in a public square in the northern state of Terengganu, one of the country's most conservative areas.
The women, dressed in white dresses and Muslim headscarves, were each given six strokes as they sat on stools in a sharia court, with one of them breaking down in tears.
Almost two-thirds of Malaysia's 31 million people are Muslims, who are governed by Islamic courts in family, marriage and personal matters. The couple received their lashings at the Shariah High Court in Kuala Terengganu, a region of Malaysia known for being highly conservative.
The two women were fined by the sharia high court on 12 August, after they pleaded guilty to committing musahaqah, or sexual relations between women.
Asked for Amanah's stand on the public caning of two alleged lesbians in Terengganu over a Shariah offence on Monday, Khalid noted that laws relating to religion in Malaysia are passed in the individual lawmaking bodies in each state.
"Under worldwide human rights law, corporal punishment constitutes a form of torture", Varughese said in a statement calling for an immediate moratorium on all forms of corporal punishment.More news: Chinese Billionaire Accused of Sex Misconduct Unlikely to Face Charges, Lawyer Says
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Malaysian women's groups Justice for Sisters and Sisters in Islam called for a review of the Sharia law.
Thilaga Sulathireh, from the group Justice for Sisters, who witnessed the ordeal, was concerned about the safety, privacy, harassment, humiliation and trauma of the women. This case shows a regression for human rights. It's not about the severity of the caning.
"The Malaysian authorities must immediately repeal repressive laws, outlaw torturous punishments and ratify the UN Convention Against Torture", the group said.
The public nature of the caning has been criticised, including by Umno's Rembau MP Khairy Jamaluddin, who said it should not have been done publicly as Islamic teachings are that the dignity of each person should be looked after.
"Sexual acts between two consenting adults should not be criminalised, let alone punished with whipping", Women's Aid Organisation said.
The caning occurred amid a climate of fear and discrimination against Malaysia's lesbian, gay, bisexual and transgender community.
Earlier last month, a minister ordered that portraits of LGBT activists be removed from a public exhibition.