The match for Russia 2018 World Cup Preliminary Joint Qualification Round 2 is slated to be played in Tehran on Thursday.
A 22-member team today left for the forthcoming game.
Six players from the list of 28 probables, including injured striker Chhetri, didn't travel with the squad.
"We had to take some bold decisions and we have to travel to Tehran without our influential captain Sunil Chhetri," national coach Stephen Constantine said.
Chhetri has been ruled out following a groin injury which he had picked up in the I-League.
"The injury is such that it requires him to take necessary care and that requires him to stay back in India and get treated," Constantine said.
A disappointed Chhetri couldn't recall as to when he last missed an international match due to injury.
"I was sitting at my room trying to recall as to when I last missed a national team match for injury. It's so disappointing. It's such an important match for us and I still can't believe that I would be missing it," Chhetri said.
"At the moment it is obviously not a good feeling to have missed the bus but maybe in the long run, it will probably be for good."
Meanwhile, Chhetri lauded Constantine's initiative of summoning Dhanpal Ganesh and Robin Singh to get their rehabs assessed, monitored, checked and advised by the medical staff of the national team.
Besides Chhetri, T P Reheneesh, Rino Anto, Allwyn George, Malsawmzuala and Md. Rafique have been dropped for the match against Iran.
GOALKEEPERS: Subrata Paul, Gurpreet Singh Sandhu, Karanjit Singh
DEFENDERS: Aiborlang Khongjee, Augistine Fernandes, Arnab Mondal, Pritam Kotal, Sandesh Jhingan, Narayan Das, Lalchhuanmawia
MIDFIELDERS: Pronay Halder, Bikash Jairu, Cavin Lobo, Rowlin Borges, Francis Fernandes, Harmanjot Singh Khabra, Udanta Singh, Vineet Rai, Seityasen Singh
FORWARDS: Jeje Lalpekhlua, Sumeet Passi, Halicharan Narzary.
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