Bosnia-Herzegovina was suspended from world football by FIFA and UEFA on Friday because its federation refuses to replace a three-member presidency with a single leader.
The ban on national and club teams playing internationally threatens to see Bosnia kicked out of UEFA's 2012 European Championship after making a promising start to qualifying.
"FIFA and UEFA deeply regret that this decision had to be taken," the governing bodies said in a joint statement. They will meet soon "to discuss the next steps required to try to bring (Bosnia) back into the football family as soon as possible."
FIFA could install an emergency panel to run the federation's affairs and allow Bosnia's teams, referees and officials to work internationally.
In recent years, the world body has appointed so-called "normalization committees" with mandates of up to 12 months in El Salvador, Senegal and Samoa.
Bosnian football is run on similar lines to its politics, and the federation's presidency is shared by a Bosniak, a Croat and a Serb.
The situation was tolerated because FIFA and UEFA were aware of Bosnia's political problems and ethnic divisions after the 1992-95 war.
Last October, the executive committees of FIFA and UEFA set Bosnia a March deadline to modernize its statutes or a suspension would be automatically triggered.
At a meeting in Sarajevo on Tuesday, Bosnian Serbs opposed the single president plan because they fear it could jeopardize their autonomy.
"Consequently, the (Bosnian federation) has lost all of its membership rights with immediate effect and until further notice," FIFA said.
Bosnia is scheduled to resume its Euro 2012 program on June 3 in Romania, which it beat 2-1 in Zenica last Saturday, and host Albania on June 7. It has never appeared at a major tournament as an independent team.