"Pakistanis are outraged by my earlier tweet. Their outburst clearly means they see terrorist and Pakistan as the same! Self-goal. Stop terrorism," Mr Adnan tweeted on Friday after receiving hate comments on his previous post.
The singer, who received his certificate of Indian citizenship earlier this year, had first tweeted: "Big Congratulations to PMO India and our brave armed forces for a brilliant, successful and mature strategic strike against terrorism! Salute."
Mr Adnan, whose father Arshad Sami Khan was a diplomat and served as Pakistan's ambassador to 14 countries, angered many Twitter users, including Salman Ahmad of Pakistani band Junoon.
"Being the son of a Pakistani ambassador should've told you that no one wins a war between nuclear states. According to your twisted logic, your father too has served as a terrorist ambassador. Have you disowned your parents too," Salman Ahmad questioned Mr Adnan.
One wrote: "Adnan Bhai you were a Pakistani and you better know the strength of Pak Army."
Another tweeted: "You don't have to keep reaffirming your pledge of allegiance to your new motherland."
A Twitter user also mentioned how his father "was in PAF and was awarded Hilal-i-Imtiaz if I wasn't wrong and you're calling them terrorist".