The police said Pramanik was arrested this morning after a woman lodged a complaint of rape with the Baguiati police station in North 24-Parganas district.
"The complaint stated that the woman athlete was a male and has been cohabiting with her for the past several months with a promise to marry her, but later denied," a top official of the Baguiati police station said.
The official said the athlete had also taken money from the victim.
He said a medical checkup in a government-run hospital would be done on Pramanik after which she would be produced in a court.
The Eastern Railway middle-distance runner had won a 4x400m relay gold in the 2006 Doha Asiad and a silver in the same event at the 2006 Melbourne Commonwealth Games.
Pramanik bagged three gold medals in the 2006 SAF Games in Colombo when she won the 400m, 800m and 4x400m relay events.
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Meanwhile, an official of the Athletics Federation of India said that Pramanik would be stripped off the medals if it was proved that the athlete was actually a male.
In an earlier incident, Pramanik was arrested under Arms Act from Habibpur Nathpara village in Nadia district on November 22, 2004 when local boys, who snatched a bag from her, informed the police that a revolver was found in her bag.