Shooting down chopper on Feb 27 was a "big mistake", the IAF chief said.
The Army has taken adequate measures to curb infiltration by deploying more troops along the Line of Control, he said.
Pakistan closed its airspace in February after a standoff with India in the wake of the Pulwama attacks that killed 40 paramilitary police.
Doval was appointed as the NSA in May 2014 in the rank of Minister of State.
Diptanshu Choudhury, a former colonel who served in the Kargil War, joined the BJP in 2016, but quit to join Trinamool Congress the next year.
Modi had said, “Can your first vote be dedicated to those who carried out the air strike.”
Modi has made national security the main plank in the Lok Sabha elections that began on April 11.
"We could have strapped their leaders to the rockets which were sent to Balakot to see the attack with their own eyes,” Fadnavis said.
"In the Balakot operation, we had technology on our side."
The letter urges the President to stop parties and political leaders from using the armed forces for their agenda.