The Football Association of Wales says the FA's plans for a 2016 British Olympic team "shows a lack of respect."
GB teams played at London 2012 but the Football Association had said that would be a one-off.
The FA has written to Wales, Scotland and Northern Ireland to inform them of its intention to form men's and women's teams in Rio 2016
"That shows a lack of respect to us as a nation," FAW's Ian Gwyn Hughes said.
|Welsh players at London 2012|
|The FAW, along with the Scottish FA and Irish FA, refused to give their official backing to Team GB in 2012. Despite their opposition, five Welsh players - Ryan Giggs, Craig Bellamy, Aaron Ramsey, Joe Allen and Neil Taylor - were named in the men's squad, with Gareth Bale ruled out of the competition through injury having been expected to take part.|
The FAW, along with the Scottish FA and Irish FA, refused to give its official backing to Team GB in 2012, and that opposition continues.
The home nations fear a Great Britain squad could set a precedent which would affect individual memberships of Fifa and the International Football Association Board.
Midway through the campaign for Euro 2016, Wales are second in their qualifying group with a realistic chance of reaching a major tournament finals for the first time since 1958.
"It [Wales' national identity] is something we should be proud of," Hughes added.
"We can't compete as Wales on a national level on many things, but sport is something that is unique and brings the best out of us as Wales.
"It gives us the opportunity to compete on a worldwide level and I don't think we should lose that opportunity."
The Scottish FA has said it is firmly against the idea, fearing participation would threaten the country's independent status within Fifa.
FAW president Trefor Lloyd Hughes said he was "livid" with the Football Association's plans to enter men's and women's Great Britain teams for the 2016 Olympics.
"If they want to work with us they have to be more open with us and they don't seem to be keeping to agreements. I'm livid about it," he said.