Kerala Women's Commission on 14 November said it has been denied permission by Hadiya's father to meet her.
Twenty-four-year-old Hadiya is currently living with her parents here, who have alleged that her marriage to a Muslim man is a case of 'love jihad'.
On November 6, the National Commission for Women (NCW), however, said Hadiya is safe and secure at her parents' home.
Talking to media outside Hadiya's home, NCW acting president Rekha Sharma said, "I just met Hadiya as the NCW was concerned about her well-being. She is in good health, is not being beaten up, she is eating, was smiling and is happy."
Four months ago, the Kerala High Court had sent Hadiya with her parents K M Asokan and Ponnamma after annulling her marriage with Shafin Jahan.
The case is under consideration of the Supreme Court now, which had ordered the NIA investigation into it.
Hadiaya's husband, Shafin Jahan on September 16 filed a plea in the Supreme Court and requested to call off the NIA probe, alleging that the investigation agency "is not being fair".
On October 30, the Supreme Court asked Ashokan to produce Hadiya on November 27, in the next date of hearing in the case.
The apex court's direction came in the backdrop of news reports that suggested Hadiya was being tortured at her parents' home.
After the Supreme Court's orders, Ashokan told media, "I welcome the order of Supreme Court. I will produce Hadiya before the court on November 27. I don't have any objection on my daughter marrying a man from other religion. But this is not a love marriage".
"The news that Hadiya is under house arrest is not correct. Two female police officers are with her 24x7," he informed.
In September, a group of people had submitted a petition to Kerala Chief Minister Pinarayi Vijayan and demanded a probe into the alleged unlawful incarceration of Hadiya.