The empty seats at events including the tennis, swimming and gymnastics have sparked anger in Britain because many people were left disappointed in the massively oversubscribed ticket ballots ahead of the Games.
Local organisers LOCOG explained that the empty seats were reserved for members of the accredited "Olympic family" – national Olympic officials, sports federations, athletes, the media and sponsors.
"Let us put this in perspective. Those venues are stuffed to the gunnels. The public are in there," Coe told a press conference.
Empty seats "in the very earliest phases" of an Olympics were not unusual, he said.
'Don't blame the sponsors'
"There are tens of thousands of people at this moment within the accredited 'family' that are trying to figure out what their day looks like, where they are going to be asked to go to, frankly working out how you divide your time."
Coe added: "I don't think you will be seeing this as an issue long-term through the Games."
International Olympic Committee communications director Mark Adams insisted that sponsors were not to blame.
He said: "It's completely wrong to say this is a sponsors issue. It's a whole range of people – federations, athletes, some media, a handful of people.
"A majority of sponsors have turned up."
Organisers were urgently seeking ways of filling any empty seats.
Soldiers, students and teachers
Soldiers involved in the security operation were given spare seats at gymnastics events on Sunday morning, while students and teachers from east London were also handed places at some unfilled venues.
A LOCOG source said the organisers were "extremely frustrated" by the empty seats.
Wimbledon's Centre Court was half-empty on Saturday for a singles match featuring a British player and on Sunday, a group of around 200 seats could be seen on the showpiece court.
There were also gaps in the stands for a second day at the swimming heats in the Aquatics Centre.
Ben Bannar-Martin, a 38-year-old banker, who was visiting the Olympic Park in east London with his wife and two daughters, said: "It's a shame. I tried to get tickets in the first ballot and I did not get any."
In contrast to the unfilled venues, huge crowds lined the streets of the route of the women's cycling road race through London and Surrey, for which tickets were not required.
Britain's culture minister Jeremy Hunt admitted the empty seats were "very disappointing".
He added: "I was at the Beijing Games, in 2008, and one of the lessons that we took away from that, is that full stadia create the best atmosphere — it's best for the athletes, it's more fun for the spectators, it's been an absolute priority.
"LOCOG are doing a full investigation into what happened. I think it was accredited seats that belonged to sponsors, but if they're not going to turn up, we want those tickets to be available for members of the public, because that creates the best atmosphere."
Meanwhile, Britain's Sunday Times newspaper reported that British police were investigating the alleged black-market sale of Olympic tickets by three official ticket agents covering the Games.
The newspaper said it had secretly filmed Olympic officials and agents offering to sell thousands of tickets for up to 10 times their face value.
Detectives launched the inquiry last week after studying more than 20 hours of recordings provided by the newspaper, the report said.
They will seek to question the official ticket agents for the national Olympic committees of China, Serbia and Lithuania, it added.
Police declined to confirm that they were probing the claims. – AFP