The Welsh coach was contacted by phone by Bosnian boss Sergej Barbarez after being drawn into a row over team selection at Danish club Brondby IF.
Cooper had been accused by Barbarez of leaving out Benjamin Tahirovic because of his nationality ahead of Wales semi-final tie in Cardiff on Thursday.
Barbarez suggested Cooper’s background had influenced the decision, claiming the midfielder himself had raised concerns.
"Benjo has told me some things that are hard to believe. It has something to do with his coach's origin," Barbarez said.
"When your coach wishes you, but not your national team, good luck, it leaves room for thought.
"He (Cooper) 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."
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The comments placed Cooper’s nationality at the centre of an increasingly tense build-up to the play-off tie, with the implication that his Welsh identity had played a role in club decisions.
The controversy has since cooled, with reports indicating Tahirovic has personally contacted Cooper to apologise, while sporting director Benjamin Schmede has also spoken to Barbarez to clarify the situation.
Tahirovic had been absent from Brondby’s last two matches, fuelling the initial claims, but the Danish club maintain the call was based solely on internal considerations rather than any connection to the upcoming international fixture.
The timing of the dispute has added an extra spice to Thursday’s meeting in Cardiff, where the winners will move on to face either Italy or Northern Ireland for a place at the World Cup.
For Cooper, whose managerial career has included spells at Swansea City, Nottingham Forest and Leicester City, the episode represents an unusual claim of a clash between club responsibilities and international allegiances.
Brondby moved swiftly to defend their manager and distance the situation from any international influence.
Communications director Soren Hanghoj dismissed the claims and insisted the decision to omit Tahirovic from recent matchday squads was made collectively within the club.
"This is quite a far-reaching speculation," Hanghoj said.
"Steve has publicly stated the considerations behind the decision -- and none of them have the slightest connection with either national team. That goes without saying.
"It is a club decision that has been made jointly by an entire coaching team and the sporting management. And there are not that many Wales fans in Brondby after all."
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