Now in charge of Brondby in Denmark, Cooper has been accused by Barbarez of sabotaging their World Cup hopes.
Barbarez has been angered by Cooper not selecting Bosnian midfielder Benjamin Tahirovic in recent weeks in the lead up to the playoff against Wales.
Speaking at a press conference in Sarajevo on Monday, Barbarez said: "Benjo has told me some things that are hard to believe.
"It has something to do with his coach's roots and origins. When your coach wishes you, but not your national team, good luck, everything is much clearer.
"He has told him that everything will return to normal after the national team season.
"I am not like that, I love and value sport and competition more."
Brondby's communications director Soren Hanghoj, however, insisted on TV 2 Sport: "This is quite far-reaching speculation.
"Steve has publicly stated the considerations behind the decision – and none of them have the slightest connection with either national team.
"It is a club decision that has been made jointly by the coaching team and sporting management.
"And there are not that many Wales fans in Brondby after all."