He said charges on IPC sections 302 (murder), 376 (rape) and 201 (destruction of evidence) have been filed against Uday Swaroop who was student of same institution.
Swaroop's alleged friend, however, has been left out of the CBI charge sheet even as the local police had booked both of them in their charge sheet.
Agra police had alleged that while Swaroop had killed the girl, his accomplice had helped him destroy all evidences of the crime.
CBI sources said while local police had charge sheeted the accomplice of Swaroop, the agency did not find any evidence against him and will recommend his discharge but the final call will be taken by the court.
23-year-old Neha Sharma, a resident of Jammu and pursuing PhD in nanotechnology, was found dead under mysterious circumstances in the institute's laboratory on March 16, 2013.
Her body, bearing 12-deep cuts inflicted by a sharp-edged weapon, was found laying in a pool of blood, with her hands tied behind her back.
The murder had sparked protests by the students of the college, where Neha was enrolled for her PhD.
Swaroop, who is at present on bail, was the student of BSc final year at the institute at the time of crime. He is a relative of a high-ranking official of the institute, who holds influential position in a religious cult, sources said.
They said local police had recovered a strain of hair which matched with one of the two suspects arrested by them and was a strong piece of evidence in the case.
The sources said the agency had taken over the probe from the local police and booked a case of murder against unknown persons.