India, the top-ranked side in the Asian 5 Nation tournament, had been expected to comfortably beat Uzbekistan in Thursday's match in Lahore but they were beaten 23-17 after being overrun by the opposition.
Aga Hussain, vice president of the Indian Rugby Football Union, said 14 members of the squad who are serving in the armed forces had been unable to gain clearance from their bosses to enter Pakistan.
"We need a military intelligence clearance for army players to travel abroad. We applied for it and we were waiting for this permission, unfortunately we did not get it," Hussain told AFP.
"As this permission was refused, we had only 12 players."
Although two members of the team management were drafted in to play alongside the 12 civilian players, the lack of numbers ultimately took its toll as the team was beaten after conceding two late penalties.
Hussain said there was no prospect of the soldiers now getting clearance, but he was hopeful that India would at least be able to field a full 15-man line-up for the next match against Pakistan on Sunday.
"One of our players, who is a student, stayed in Delhi for his exams but he has a visa and will try to join the team today."
Sporting ties between India and Pakistan often fall foul of diplomatic tensions between the two neighbours.
India's cricket team has not toured Pakistan since 2006 although it did host a one-day series in 2012-13.
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@sridhar: LOL of all the places to play rugby in. Countries are issuing travel advisories against travel to Pakistan, Pakistanis themselves are getting out and here we have the Indian rugby team going to play. Have some sense guys else invest heavily, in insurance.
This is a conspiracy to prevent India from winning the tournament !! 1. We will complain to the UN. 2. We will complain to Katrina Kaif. 3. We will complain to Gullu Butt. Totally unfair. So what if the Indian soldiers spy on the Rugby ground? There are no nukes under there, are they?
You idiots should have cancelled your visit to Pakistan. The visa regime has been taken to a ridiculous extent. Indian govt should not participate in any sporting event in pakistan just for reasons of security. pakistan is in a civil war for god's sake.
The title of the news item is misleading the Indian players have not been allowed to enter Pakistan by the Indian Army.