The Football Association insist they have letters from the other home nations accepting their right to select Scottish, Welsh and Northern Irish players for British Olympic football teams.
The three other home associations are adamant they are not party to the ''historic agreement'' announced by the British Olympic Association on Tuesday.
FA general secretary Alex Horne said: ''We have been very clear since the Olympic games were awarded to London that the FA is committed to Team GB football teams. We have been flexible in working with the BOA and other home nations regarding the makeup and selection for these teams being a collective of all home nations, or all English sides.
''It is clear that under the Olympic Charter there has to be a non-discriminatory selection process for all players. These are not the FA rules.
''We are sensitive to the concerns of the other home associations in relation to each of our individual identities, and we have been assured by FIFA there is no threat to each association. However as an organisation the FA has been mandated by the BOA to organise a men's and women's team for the 2012 Olympic football tournament across the UK.
''All three associations have notified us in writing that they acknowledge that legally we are entitled to support the BOA in the selection process.''
The sale of 1.7 million Olympic football tickets will begin on Friday but the BOA insist that has ''absolutely no bearing'' on the timing of their announcement.
Scottish FA chief executive Stewart Regan said he had emailed Horne as recently as Monday night stating their opposition and was stunned to see the announcement.
Regan said: ''I sent Alex Horne an email saying we could not support or endorse the Team GB but that we recognised from a legal position we couldn't stand in the way of a player opting to play for Team GB.
''I asked if we could be kept in the loop so to see an announcement made today came as a shock to me and all the other associations. None of us knew this was going to happen. We are very surprised and disappointed.''
The BOA said the FA had consulted the other associations about player selection. A 'long list' of players from across Britain will be drawn up by the managers of the men's and women's teams, and the players each asked to confirm their availability. An announcement of the two squads of 18 players in the summer of 2012.
The British men's team will be made up of Under-23s but three over-age players are also allowed. The women's team can be of any age.