"If FIFA and UEFA suspend us and prevent the national team from playing in the next qualifications, there will be no reason for me to remain as the coach," Susic told the Dnevni Avaz daily in an interview. "I will leave the national team."
The NSBIH's general assembly failed to replace on Friday the tripartite inter-ethnic presidency with a single president as requested by football's ruling bodies, risking suspension that could prevent Bosnian teams from taking part in international competitions.
UEFA and FIFA delegates immediately left the session, saying that their executive committee would decide on measures against the NSBIH.
NSBIH, formed after the 1992-95 Bosnian war ended and the country was divided into two ethnically divided regions, has been run by a three-person presidency whose members are chosen on ethnic rather than professional criteria.
Susic, who took the job in December from Croatian Miroslav Blazevic, said he would appeal to UEFA officials not to make a hasty decision that would destroy Bosnian football.
"It's known that UEFA forbids any form of political interference into the work of the Football Federation, and it is obvious that what happened has nothing to do with sports but with politics," Susic told the Mostar-based Dnevni List daily.
Bogdan Ceko, the Serb member of the NSBIH three-person presidency which also includes the Muslim and Croat members, said however that he did not believe that football bodies would suspend NSBIH.
"We know that UEFA emergency board will meet, and I shall be involved to see how we can resolve this," Ceko told the Oslobodjenje newspaper.
The Serb delegates in the NSBIH assembly voted against the abolishment of the tripartite presidency, the Muslims voted for and most Croat delegates abstained from voting.
Milorad Dodik, the prime minister of Bosnia's Serb-dominated region who is known for separatist rhetoric, said over the weekend that the Serb Republic should form its own Football Federation. Bosnia also comprises the Muslim-Croat federation.
Football fans across Bosnia have long protested against the NSBIH's organisational structure and some players have boycotted the national team.
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