Another person, Vijay Dubey, who had been named as an accused in the case, was discharged by the CBI court.
October 27, 2010, Arya, the then chief medical officer of Lucknow, was shot dead near his residence.
Uttar Pradesh police was earlier investigating the murder, but the case was subsequently handed over to the CBI.
According to the prosecution, Dr Arya's killing was related to the National Rural Health Mission scam.
The court has fixed May 3 as the next date of hearing.