Bosnia sacked coach Safet Susic on Monday following a series of poor results in Euro 2016 qualifiers.
"The situation is worrying since the goals set for the first part of qualification have not been met," a Bosnian football federation statement said.
"Qualifying for Euro 2016 is under question and the federation`s executive committee has unanimously decided to sack coach Safet Susic and his aides."
On Sunday, Bosnia, lacking several first-choice players such as strikers Edin Dzeko and Vedad Ibisevic, were defeated 3-0 by Israel.
They have failed to win a single qualifying match following a 2-1 defeat to Cyprus draws against Wales (0-0) and Belgium (1-1).
Upon his return to Sarajevo from Israel, Susic, the first ever coach to lead a Bosnian side to a major tournament finals when they qualified for the World Cup in Brazil earlier this year, told reporters he would like to stay on.
"I said before this match against Israel, and I repeat, I don`t want to quit since I believe there is still a chance to go to the Euros. It is a small one, but it exists," he had said.
Bosnia are currently fifth in their Group B with two points while Israel lead on nine points.
The 59-year-old Susic, who apart from two appearances for his home country played 54 internationals for Yugoslavia, had been in charge of the Balkans country since 2009.
France Football magazine voted him Paris Saint-Germain`s best player of all time in 2010 -- he scored 85 goals in 345 appearances -- and then two years later as Ligue 1`s finest ever foreign player.
Susic had signed a two-year extension to his Bosnia contract in July following the World Cup.