Pinki Pramanik was arrested on Thursday following the complaint lodged by the woman who said she was the live-in partner of the athlete, Subrata Bandopadhyay, a deputy commissioner with West Bengal police, said.
"In her complaint, the woman levelled rape charges against Pramanik. She said they have been living together for quite a while," Bandopadhyay said.
Police have obtained a court order for a medical test to prove Pramanik's gender, Bandopadhyay said, even though the former athlete is opposing it.
"I have undergone numerous tests in my career as an athlete. Why should I agree to more ridiculous tests?" she was quoted as saying by Times of India.
Another 2006 Asian Games medallist, Santhi Soundarajan, was stripped of the women's 800 metres silver medal after failing a gender test and the Athletics Federation of India is shocked at the possibility of a second such embarrassment.
"It's a tricky situation now and we are waiting for an official report on her medical test," AFI secretary C.K. Valson said.
"We can't take any decision unless we have the report with us."
However, Valson was not sure if Pramanik risked losing her medals even if medical tests went against her.
"I don't think she can be stripped of the medals she won six years back. A lot of physical changes can take place in those six years," Valson said.
"We never had any such complaint against her when she was an active athlete and naturally there was no question of subjecting her to a gender test.
"You can't put an athlete through gender test unless and until another athlete has accused her of being a male," added the AFI official.