The football tournament has proved one of the hardest sells for the Olympics, despite several high-profile players such as Ryan Giggs taking part.
There were originally 2.5 million football tickets on sale and Olympic organisers have sold more than half of them.
Organisers said its move would not impact on its target to raise around £500m from Olympic ticket sales.
The majority of the withdrawn football tickets are priced at £20.
Games organisers said the reduced capacity in some stadiums would manifest itself by not using a tier or areas of a ground in some of the venues.
In the past few months, in an effort to avoid the embarrassment of empty stadiums, the organisers have carried out a print, outdoor and digital campaign to showcase the Olympic football tournament.
Matches will take place at Wembley Stadium and in Newcastle, Glasgow, Coventry, Cardiff and Manchester.