Among the two arrested is nephew of Ahmed's brother-in-law Rehan, Inspector General of Police (Bareilly Zone) Vijay Kumar Meena told a press conference here.
The alleged mastermind, identified as Muneer, is still at large and will be nabbed soon, Meena said.
Giving details, the IGP said the accused followed the 45-year-old NIA Deputy SP on motorcycle after a wedding reception of a relative on the intervening night of April 2 and 3.
The attackers overtook his vehicle at Sahaspur village and Muneer allegedly fired at Ahmed, killing him on the spot, he said. His wife was critically injured in the shoot out, but his two children escaped unhurt.
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Along with Rehan, his accomplice Zainul was also arrested.
About the motive of the crime, Meena said it was borne out of domestic dispute, family matters and share in a property deal.
The killers had pumped as many as 24 bullets into Ahmed and four into his wife Farzana, as their 14-year old daughter and 12-year old son watched the gruesome incident from the back seat of the Wagon-R car in which they were travelling.
In the beginning, police termed the killing of Ahmed, posted as Inspector initially with the NIA's intelligence wing and later in its investigation department, as a "planned attack" and did not rule out the possiblity of a terror angle behind the shootout.