Public canings were introduced in Aceh in 2005 and are supported by many Acehnese.
Aceh is the only province in majority-Muslim Indonesia that follows Islamic law and imposes public caning for crimes like theft, gambling and adultery.
"Even though the caning did not injure them [the women], they said it caused pain within them."
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.
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.