The firm threw in the towel last week, allegedly over fears the scheme is being scaled back to help keep the mushrooming Olympic budget under control.
FOA confirmed it had resigned from the masterplanning team - which includes EDAW, Buro Happold, Allies and Morrison and HOK Sport - but refused to comment on rumours of in-fighting among the major players.
A spokesman said: 'FOA has chosen to focus on competitions for specific Olympic projects, where it will be best placed to deliver value to the design of the Games and its legacy.'
The firm said it intended to remain on the shortlist to design the Olympic velopark.
The Olympic Delivery Authority (ODA) insisted it was too early to confirm whether it was seeking to replace FOA. It is understood there is at least six months' worth of work left to do on the masterplan, which is now in the detailed design phase.
'FOA helped us produce the masterplan, which is our vision and route map to 2012 and we thank them for all their hard work and help to date,' said an ODA spokesman.