Shukla was arrested here late last night on charges of conspiring to kill Arya, a CBI spokesperson said.
According to the CBI, the alleged motive behind the murder was the fear of being exposed for misappropriation of funds in the National Rural Health Mission (NRHM).
There were indications emerging that Shukla could also be allegedly involved in killing of another Chief Medical Officer B P Singh, official sources said.
Arya was murdered while he was taking a morning walk on October 2010 at Vikas Nagar area while Singh was shot dead in April last year at Gomti Nagar.
The agency claimed that evidence also indicated that former Deputy Chief Medical Officer Y S Sachan, whose death inside jail created a sensation, was also alleged to be a co-conspirator in the murder of Arya.
Shukla was earlier arrested by the CBI last year in connection with the NRHM scam but was granted bail by the Allahabad High Court.
The court had on July 27 directed the CBI to probe the murders of the two CMOs and also irregularities in implementation of the NRHM.
