The tension increased when players exchanged words during last Sunday's clash, with India filing an official complaint over gestures made by Pakistan duo Haris Rauf and Sahibzada Farhan.
Agha said the lack of handshakes had left him perplexed.
"I have been playing competitive cricket since 2007 and have never seen a game go without a handshake," Agha said on Saturday, speaking for the first time on the controversy.
"It is not good for cricket. Even in worst times between Pakistan and India, players have shaken hands. My father is a great fan of cricket, and he never told me that such a thing happened."
Agha said players must be careful not to cross the line when it comes to discipline.
"I think every individual has his own style. If someone wants to be aggressive on the ground, then why not. If you control the aggression of a fast bowler, then nothing is left.
"Every player knows how to deal with his emotions. I give free hand to my players to react on the ground unless he is disrespecting other players and the country."