The two federations had hoped to put together a successful bid to become joint hosts of the tournament which by then will have been extended to 24 teams.
Stadiums such as the Liberty and Cardiff's new stadium were lined up to host some of Europe's top stars but the economic downturn has been cited as one of the reasons why the bid will not get past the stage it has currently reached.
A statement on the FAW website read "After careful consideration, the Football Association of Wales and the Scottish Football Association have decided not to make a joint bid to host the Euro 2016 Football Championships."
FAW secretary general David Collins explained: "The current economic downturn and the very considerable implications for infrastructure provision following Uefa's decision to expand the European Championship finals to 24 teams are key considerations.
"While the ambition to host a future tournament remains undiminished, the unanimous view is that a bid for Euro 2016 is premature and will not maximise Scotland and Wales's chances of success."
Deputy First Minister and Minister for Economy and Transport, Ieuan Wyn Jones said: “The Assembly Government has been looking at the potential investment required to support a bid to host this tournament.
Currently only the Millennium stadium meets UEFA's requirements for this expanded tournament, and the cost of bringing other venues up to this standard would run into tens of millions of pounds. In the current economic and financial climate this is unaffordable.
We will continue to work hard at bringing world class events to Wales, which can provide economic and cultural benefits to our nation.”