It said an initial 3,000 tickets - including 600 gymnastics tickets - were "put back into the pot" and sold on the London 2012 website on Sunday night.
More tickets returned by sports federations would be released the night before events, Locog added.
Transport chiefs say London's morning rush hour went well on the first full working-day of the Games.
Prime Minister David Cameron, meanwhile, said the empty seats were "disappointing" but not "a unique episode" with other previous Games facing similar problems.
At some venues, seats in the accredited "Olympic family" areas - reserved for groups including officials, sports federations, athletes, journalists and sponsors - have remained empty.
Locog communications director Jackie Brock-Doyle said organisers were doing everything they could to fix the problem.
Diver Tom Daley is hoping to win his first Olympic medal later "We're doing this session by session, talking to the accredited groups - including obviously broadcast media and everybody else - and asking whether we can release, for the different sessions, tickets back into the public pot," she said.
And she said accredited seating for London 2012 was down 15% on previous Games.
Culture Secretary Jeremy Hunt said: "Often these are very nice seats in very high-profile positions - and so what we're saying to the IOC and the International Sports Federations is if you're not going to use them, could we have as many as possible back, because, of course, we've got lots of members of the public who would dearly love to go."
He said contractually the seats belonged to the sporting bodies, so it was a process of negotiation to get them released.
He said organisers were looking at whether it was feasible to impose a 30-minute rule whereby empty seats were re-allocated if ticketholders had not sat down within 30 minutes of an event starting.
In other Olympic developments:
Olympic organisers say their drug-testing programme targets athletes who show "enhancements in performance"PM David Cameron, who chaired the daily Olympics security meeting on Monday morning, said he travelled on the Tube "to see what the traffic situation was like". The Bakerloo line was "doing all right", he saidTeam GB's Katherine Grainger and Anna Watkins clocked an Olympic record time of 6mins 44.33secs in the women's double sculls rowing as they powered into the finalWeightlifter Zoe Smith, 18 years old and at her first Olympics, set a new British clean and jerk record and new personal best totalThe Olympic cauldron was extinguished overnight - although the Olympic flame was kept alight in a miner's lantern - while it was moved from the field of play to the south end of the Olympic StadiumTen people have been charged with ticket touting offences since the start of the Games, and a further 19 have been arrested, Scotland Yard said Medal hopesTransport for London's Games transport director Mark Evers said the network had worked well on Monday morning.
London Bridge station is expected to be particularly busy later with thousands of spectators heading to the Olympic Park and equestrian events in Greenwich.
Continue reading the main storyIt has not been such a manic Monday so far.
London workers seem to have heeded warnings that extra restrictions and Games Lanes, combined with spectator congestion might result in nightmare commutes, and have changed their patterns.
Roads seem no more jammed than normal, train and tube lines are running well.
Even at London Bridge, where passengers have their own Olympic time trial today - diverted away from the usual routes in case of overcrowding - there were no complaints.
But this is a marathon, not a sprint.
Six platforms at London Bridge will be exit only this evening as 50,000 equestrian spectators all head home from Greenwich Park during the evening peak.
And the crunch transport test comes on Friday - the first full day of athletics in Stratford's 80,000-seat Olympic stadium.
But Steve McNamara, general secretary of the Licensed Taxi Drivers' Association - representing London cabbies - complained of "chaos" on London's roads as a result of 30 miles of Games Lanes for the use of the Olympic family.He told BBC News "tens of thousands of Londoners are stuck in gridlock traffic" while Games Lanes were "completely empty".
However, London Mayor Boris Johnson said some of the Games lanes had been "turned off", allowing the public to use them, because so many Olympic officials were opting for public transport.
He said IOC president Jacques Rogge had travelled by Docklands Light Rail instead of car.
Olympic organisers expect 1 million extra visitors to London to make some 3 million journeys on public transport - on top of the usual 12m daily public transport journeys.
In competition, Team GB divers Tom Daley and Pete Waterfield are aiming for medals in the men's synchronised 10m platform final, which begins at 14:55 BST.
And Britain's men, who have made history after qualifying in third place for the gymnastics team final - ahead of Olympic and world champions China - will compete at 16:25 BST.
Mexican waveMeanwhile, Locog says it has checked all seating at temporary Olympics venues after BBC News website readers said flooring below seating at two sites had collapsed.
Michael Page, from Kent, was at the Riverbank Arena watching hockey on Sunday.
He said: "The crowd did a Mexican wave, one row jumped up and the empty seats behind moved forward which meant the flooring collapsed."
Officials drilled the flooring back together before the area was taped off, he added.
Locog's Ms Brock-Doyle said the welding had broken "on one seat at Eton Dorney and on a couple of other seats at the hockey so Games organisers have checked all the seats provided by the contractor to temporary venues".
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Olympics 2012: BBC Sport unveils new-look internet video for Games
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Lone Beijing spectator, 2008, and in Athens 2004, two fans among empty seats