Pinki Pramanik has been charged with rape after medical reports proved that the athlete is male.
The tests were conducted at SSKM hospital in Kolkata.
The police have submitted a chargesheet against Pramanik at a Barasat Court alongside the medical report.
A district court had earlier granted bail to the former Indian athlete after Pramanik was accused by her live-in partner, a divorcee and a mother of one, of being a male who repeatedly “raped and tortured” her.
The athlete had twice undergone gender determination tests in two different government hospitals but on both the occasions the tests were inconclusive. This time however, the tests have proved conclusive.
Pramanik retired from athletics three years ago and won gold in the 4×400 metres relay at the 2006 Asian Games in Doha in Qatar.
The runner was also a silver medallist at the Melbourne Commonwealth Games the same year.
Pinki had received much support from other athletes when news of the case first broke. Women's right group Maitree had written to the West Bengal Human Rights Commission (WBHRC) to keep an eye on investigations — alleging that male police officials escorted Pramanik and she was kept with male inmates and made a public spectacle.