"It's a big setback for sports in the country," Indian Olympic Association secretary general Rajeev Mehta told Reuters.
"We've been in constant touch with the government, trying to explain to them and convince them to grant visas to the Pakistani shooters. This is really unfortunate."
Last year, a boxer from Kosovo, which India does not recognise as an independent state, was denied visa for the women's world championships in New Delhi.
Boxing's governing body AIBA criticised the decision and warned it might reopen the bidding process for the 2021 men's championship due to take place in India.
"It's really unfortunate that it happened again," Mehta said.
"I spoke to IOC officials last night and the impression I got is that there could be more trouble for us. We at IOA will discuss the crisis with the government and try to find a way out."
It is unfortunate that the IOC suspension of India should have happened at a time when the sports ministry is headed by Rajyavardhan Singh Rathore, himself an Olympic silver medallist in shooting
The Pakistani shooters were scheduled to take part in the 25m pistol event and the IOC said two spots at next year's Tokyo Olympics that had been up for grabs in that competition had been revoked.
The International Shooting Sport Federation said on Wednesday it faced "an urgent situation as Pakistani athletes cannot get entry visas to participate in the competition" because of the Kashmir attack.
The IOC said Olympic berths would still be on the line in other events.
"The IOC restricted the withdrawal of recognition as an Olympic qualification event to the 25m rapid fire pistol competition in which the two Pakistani athletes were supposed to participate," it said.
"This happened in the interest of the other 500 athletes from 61 countries participating in the other events who are already in India for their competition."
It is unfortunate that the IOC suspension of India should have happened at a time when the sports ministry is headed by Rajyavardhan Singh Rathore, himself an Olympic silver medallist in shooting at the 2004 Athens Games (for men’s double-trap) and someone who has first-hand experience of all the norms for all Olympic-related events.
While the visas are issued by India’s ministry of external affairs, the failure to give visas on time to the Pakistani team for an Olympic-related event reflects poorly on the lack of coordination between ministries of the Government of India, the National Olympic Committee and the National Rifle Association of India.
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