This has been done on the directives of the Supreme Court.
The SIT will look into the two cross-FIRs filed in the high-profile case.
A statement issued by the UP Home Department said: "A decision has been taken by UP Chief Secretary R.K. Tiwari to constitute an SIT, which would be headed by IG (Public Grievance) Naveen Arora."
Directions have also been issued by the state government to include policemen with a clean image in the probe panel.
"This SIT will ensure impartial investigation into the two cross FIRs filed in the Shahjahanpur case and also probe the allegations levelled," the statement said.
Instructions have also been issued to Divisional Commissioner, Bareilly, and Vice Chancellor of the Mahatma Jyotibha Phule Ruhelkhand University, Bareilly, to ensure the admission of the law student and her brother at the university or any other affiliated college.
Directions have also been issued to the Superintendent of Police, Shahjahanpur to provide adequate security to the student, her parents and other members of her family, it said.
The move by the UP government comes a day after the Supreme Court directed it to set up an SIT, headed by an IGP-rank officer, to investigate the charges levelled by the woman.
The apex court had said that an Allahabad High Court bench will monitor the probe.
The law student had gone missing after levelling allegations against Chinmayanand in a video and was later found in Rajasthan by UP Police.
The apex court said the woman had raised certain grievances against the institution where she studied and her mother and father had some apprehensions about the safety of their children.
The top court said the Delhi Police will accompany her parents to their residence in Shahjahanpur and the woman will continue her stay in the national capital till September 12.
The matter was listed for further hearing on September 5.
The Shahjahanpur police had on August 27 lodged an FIR against Chinmayanand after the student went missing following her allegation in a video clip that he had been harassing her. She also spoke about threat to her and her family's life in the video clip.
The woman's father had alleged that she went missing at the behest of the 72-year-old BJP leader, who heads Mumukshu ashram. She is a post-graduate student in one of the colleges run by the ashram.
( With inputs from IANS )