A three-judge bench headed by Chief Justice Iftikhar Chaudhry asked Rinkle Kumari alias Faryal Bibi, Lata Kumari alias Hafsa Bibi and Asha Kumari alias Haleema Bibi to inform the court registrar's office whether they want to live with their husbands or their families.
The bench ordered police to provide complete security to the women and warned that police officials would be held responsible for negligence if they were harmed. The court said the women were old enough to make the right decisions for themselves.
The women were later taken to the registrar's office for recording their statements.
The Supreme Court also directed authorities to submit a report in two weeks on the implementation of its orders in the case.
The parents of the three women expressed disappointment at the judgment, saying they had been denied justice. The three women have been at the centre of a controversy over the alleged abduction and forcible conversion of Hindu girls and women in southern Sindh province.
In the case of 19-year-old Rinkle Kumari, rights groups and civil society activists have alleged that she was abducted by persons with links to Pakistan People's Party parliamentarian Mian Abdul Haq alias Mian Mithoo.
Mithoo and his brother have been accused of kidnapping and converting several Hindu women in Ghotki area of Sindh.
Rights activists have alleged that these women were forcibly married to Muslim men.
Matters were further compounded when Rinkle made different statements during news conferences and her appearances in court.
The apex court had earlier sent Rinkle and Lata Kumari to a women's shelter in Karachi to give them time to decide about their future free from pressure.
The court gave its ruling today in response to a Constitutional petition filed by the Pakistan Hindu Council. Ramesh Kumar, patron-in-chief of the Council, had approached the court to direct authorities to recover the three Hindu women.
Rinkle's family has said that she was abducted and forced to convert and marry a Muslim man. A similar claim was made by Lata's family.