Rawat, 55, was disqualified as a legislator along with eight Congress MLAs after they revolted against Uttarakhand's Harish Rawat government.
The FIR against Rawat was registered at the Safdarjung police station following a complaint by the woman who alleged that the former minister raped her at his residence in the posh Green Park area yesterday, a senior police officer said.
The woman today reiterated her allegations in a statement recorded by a magistrate under Section 164 of the CrPC.
This was not the first time the woman has alleged rape by Rawat. In 2003, she had accused Rawat of fathering her son.
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She had registered a case against him in Dehradun, following which he had to step down as minister in the then Congress government in Uttarakhand, the sources said.
Rawat, however, was given a clean chit in the 2003 case by the CBI.
BJP today defended Rawat, contending that his vocal politics may have prompted his adversaries to lodge the case.
"Harak Singh ji has an extremely vocal style of politics due to which he is constantly in the limelight. This may have made his political adversaries come up with a 'made-up' case," Uttarakhand BJP spokesman Munna Singh Chauhan told reporters.
Chauhan said that the police should be allowed to investigate the case, though he hinted at a conspiracy.
"We don't have the details of the case yet, police should be allowed to investigate the case and law should take its course. But the possibility of a conspiracy behind this cannot be ruled out. Earlier also similar complaints involving women have been lodged against him but in each case he either got a clean chit or the complainant later withdrew," he said.