"It was carried out perfectly," Hishamuddin said in a statement. "Even though the caning did not injure them [the women], they said it caused pain within them."
Two of the women were whipped six times while the third received four strokes of the rotan (cane).
He said one woman was released from prison on Sunday, another will be freed in the next few days while the third will go free in June.
The women, and four men, were caned following a decision in the religious courts in December, Hishamuddin said.
His comments are being seen as a signal that the authorities could be preparing to cane another Muslim woman, Kartika Sari Dewi Shukarno, who was arrested last year for drinking beer and sentenced to six strokes of the cane.
|Kartika's sentence came under review following widespread criticism [AFP]
Kartika's case, which was to have been the first time a woman was caned under Islamic law in Malaysia, is under review following widespread publicity and international criticism.
The case, when first reported, raised concerns that the nation's secular status is under threat, eroding the rights of some 40-45 per cent of the country's ethnic minorities.
Hishammuddin said Kartika's case had flagged concerns about how women should be flogged and that the recent canings demonstrated that the prisons department can carry out punishments in accordance with Islamic law.
Under the sharia, the women have to be whipped in a seated position by a female prison guard and be fully clothed.
"I hope this will not be misunderstood so much that it defiles the purity of Islam," Hishammuddin said, according to state media.
"The punishment is to teach and give a chance to those who have fallen off the path to return and build a better life in future."
The caning, however, has raised new questions about whether a state religious court can sentence women to be caned when federal law precludes women from such a punishment, while men below 50 can be punished by caning.
Malaysia has a dual-track legal system with Islamic criminal and family laws, which are applicable only to Muslims, running alongside civil laws.
"It's not as if this is the Middle East... it's not a good signal that they [the government] are sending out. The fact is that any form of whipping is barbaric"
Ragunath Kesavan, Malaysian Bar president
News of the women's caning sparked public outrage, with lawyers and rights groups on Thursday blaming the government for allowing it.
Ragunath Kesavan, president of the Malaysian Bar, said it was worrying that the punishment had gone ahead even as the caning issue was being hotly debated by Muslim scholars, religious groups and human rights activists.
"The impression was that Kartika's case would be the first so I've got no idea what has happened," he said.
"It's not as if this is the Middle East... it's not a good signal that they're [the government] sending out."
"We are against any form of corporal punishment, for men or women," Kesavan said. "The fact is that any form of whipping is barbaric."
The case is expected to fuel a debate over rising "Islamisation" in Malaysia, where religious courts have been clamping down on moral offences, as well as a ban on Muslims consuming alcohol that had been rarely enforced.
London-based human rights watchdog Amnesty International on Wednesday urged Malaysia to end a caning "epidemic", saying the women's case was "just the tip of the iceberg".
Donna Guest, the group's deputy Asia-Pacific director, said in a statement that Malaysian authorities caned more than 35,000 mostly foreigners since 2002.
"The government needs to abolish this cruel and degrading punishment, no matter what the offense," she said.
Sisters in Islam, a local group of Muslim women activists, said the caning "constitutes further discrimination against Muslim women in Malaysia".