But late on Monday a chief judge with the court announced that the sentence would be upheld.
Reacting to the news Kartika's father, Shukarno Abdul Muttlib, said that while the family had yet to be informed of the court's decision, his daughter "accepts the punishment" and would like it to be carried out as soon as possible.
"We obey the law [and] it's a challenge ... [but] it's the way of my life," he told the Associated Press.
No date has yet been set for the caning.
Kartika, a former nurse turned part-time model, was sentenced in July to six strokes of the cane and a fine of $1,400 for drinking beer in 2007 at a beach resort.
She had pleaded guilty in her original trial and had refused to appeal her sentence, despite an intervention from the Malaysian prime minister who said she would likely receive a sympathetic hearing if she did so.
The case had caused an uproar in the media and among rights activists.
Malaysia has a large Chinese and Indian community, but uses a dual-track legal system where sharia courts can try Muslims for religious and moral offences under Islamic law.
Alcohol is widely available in the country but is forbidden for the majority Muslim community, who make up just over half the population.
The actual caning is expected to be carried out using a thin stick on the back and would be largely symbolic rather than aimed at causing pain.
Caning under Malaysia's criminal law, used in the case of convicted rapists and drug smugglers, uses a thick rattan stick applied with heavy force on bare buttocks that causes the skin to break and leave scars.
Nonetheless rights groups have said that even a gentle caning raises the broader question of the role of Islam in the justice system and whether Islamic laws should intrude into people's private lives.