The police action came after it submitted in a court a medical report on the gender determination tests which showed that Pinki, now on bail, is a male.
Based on the report of the medical test done by a board of doctors at the state-run SSKM hospital in Kolkata, the police filed a charge sheet against Pinki charging the athlete with rape and cheating as well as accusing her of holding out threats.
Pinki was accused by her live-in partner Anamika Acharya of being a male who raped her, which led to Pinki's arrest on June 14 and an order for medical examination to confirm the gender was issued.
The former middle-distance runner, who won the 4x400 m relay gold in 2006 Doha Asian Games, was freed from jail on July 11 pending disposal of all cases.
Pinki's earlier reports of gender tests were inconclusive both at a private nursing home at Barasat as well as at Barasat general hospital.
The case was referred to the state-run SSKM hospital, but facility for chromosome pattern test was unavailable there too. Later, the test was concluded at Hyderabad, police said.
The athlete's arrest and imprisonment earlier sparked an outcry across the state over gender discrimination and the manner of conducting the tests.