"Chief Minister Ashok Gehlot has given a direction to the home department for referring the case to the CBI," a government spokesperson said.
At present state CID is probing the case.
53-year-old Nagar, who was Minister of State for Dairy and Khadi in the Gehlot government, had put his papers on September 19 after a 35-year-old woman alleged that she was raped by him.
The woman had alleged that the minister, who had helped her in the past, called her to his house on September 11, promising to get her a job. On some pretext, the minister took her into a bedroom and raped her, she alleged.
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He has admitted that the woman had come to see him. "When she came at 5 pm I was surrounded by people, I met a lot of people then," Nagar said, adding he is being framed by his political rivals.
Sodala Police station had booked Nagar for allegedly raping, threatening and beating up the woman.
After registering the case under various sections of the IPC, police had referred the case to the CID crime branch since it involved a sitting MLA.