Around 40 spectators with general admission tickets shouted angrily and demanded to know why they were being denied entry.
The main draw appeared to be India's Abhinav Bindra, who won independent India's first individual gold in 2008 in the event.
"I've come all the way from India just to watch this match ...spending such a huge amount," Mohinder Lal, who said he was an Indian shooting official, told Reuters.
"Now they won't let me in."
A venue manager told Reuters the problem was that ticket-holders did not understand that "general admission" tickets meant that seats for some qualifying events would be allocated on a first-come, first-served basis.
The surplus demand contrasted with other events at the London Games, which has been blighted by numerous empty seats, angering ticketless fans.
With an hour gone of the 105-minute rifle qualifying session, approximately 80 spectators were queuing outside the indoor range after being told by organisers that a one-in-one-out policy would be used for fans hoping for a glimpse of the 47 rifle shooters in action.
Part of the crowding was due to a heavier than expected turnout by media, but the governing International Shooting Sport Federation (ISSF) said they could not help.
"We are not involved in ticketing options and we don't know exactly how it works," an ISSF spokesman said, adding the huge media interest was a surprise. "We didn't expect such a huge number of media coming and following the qualification."
He said 108 nationalities were represented, the highest ever, placing shooting in the top five Olympic events.