The Croatian Football Federation (HNS) has sacked Ognjen Vukojevic after the former international appeared in a social media video with Domagoj Vida and allegedly made pro-Ukraine remarks.
Vukojevic and Vida made comments including "Glory to Ukraine", a phrase that has been adopted by anti-Russian nationalists, after Croatia beat the World Cup hosts on penalties to book a semi-final against England.
FIFA opted not to suspend Vida, warning the centre-back over his conduct following the incident, while the Besiktas defender insisted the video was not intended as a political statement.
HNS, though, announced on Monday that Vukojevic has been removed from his position as an associate of the Croatia coaching staff, with his World Cup accreditation also revoked.
A statement said: "HNS hereby apologises to the Russian public for the actions of a member of the Croatian delegation.
"Ognjen Vukojevic and Domagoj Vida likewise apologise for their statements, which were in no way intended to have political connotations, yet which unfortunately left room for such interpretations."
Vukojevic issued a release accepting his dismissal but he continues to deny intending to make anti-Russian remarks.
"I would never want to be a burden to the national team, especially not ahead of a match as monumental as the World Cup semi-final, when the team is most in need of a peaceful atmosphere," Vukojevic said.
"My statements were truly not intended to have any political connotations, and my only intention was to thank my friends in Ukraine for their support, and to thank my club, Dynamo Kiev, for permitting me to participate at the World Cup.
"However, I understand that my statements unfortunately could have been interpreted differently, for which I am sorry. I apologise to the Russian public if they have understood my statements in such a way.
"I am extremely proud of what Croatia has done in Russia so far, and I wish the boys the best of luck for the rest of the tournament. I will be their biggest fan until the very end."
Croatia take on England in Moscow on Wednesday for the right to play either Belgium or France in the final.