Armita Geravand's arrest was first published by IranWire on Monday, with sources telling the outlet she suffered from "visible head injuries" and need to be resuscitated after arriving at Fajr Air Force Hospital in a comatose state.
The Hengaw Organisation for Human Rights later said the 16-year-old had been in a coma since Sunday due to a "severe physical assault".
Ms Gerawand's family, from the Kurdish city of Kermanshah, have been prevented from visiting her at hospital, Hengaw said.
A journalist who visited the site to report on the incident was detained by authorities.
Footage circulating on social media shows the young woman, who appears to be unconscious, being carried out of the metro carriage.
State news outlet Irna has reported she suffered a drop in blood pressure and published videos of her parents supporting official reports.
Rights groups have said her family have been pressured into denying she was beaten by morality police officers.
Families of detained and killed protesters and regime critics are often subject to surveillance, threats and arrest for criticising Tehran.
Dozens of grieving relatives were arrested ahead of the first anniversary of the protests last month, including Mashallah Karimi, whose son was executed in January.
Iran has tightened hijab laws since the protests, which require women to cover their hair and wear loose-fitting clothes in public.
Women have been barred from their work and universities for not wearing the hijab, while Tehran's extensive metro system had also threatened a similar ban.
Passengers have reported being turned away from ticket gates for not wearing the hijab, while increased morality police patrols have been noted on the streets.
Last month, parliament passed a "hijab and chastity" bill that rights groups have condemned as gender apartheid.
Under the legislation, which is yet to be approved by Iran's Guardian Council, women face a 10-year prison sentence for not wearing the hijab.
The new legislation also states children can also be prosecuted, and toys must also conform to the law.