The Ukrainian club says it has lost the chance to recoup funds by selling foreign players abroad.
Ukrainian football club Shakhtar Donetsk is reportedly seeking €50 million in damages from FIFA over its temporary transfer rules.
Foreign players and coaches at Ukrainian clubs were allowed to suspend their contracts and sign for other teams this month amid the war.
The Ukrainian club has now appealed FIFA decision's to the Court of Arbitration for Sport (CAS), according to The Athletic (subscription required).
Professional football was suspended in Ukraine after Russia invaded the country on 24 February.
Shakhtar -- who were top of the league -- were hoping to sell some of their 14 foreign players to generate funds amid financial losses from the league's suspension. But FIFA's decision on June 21 to open an extraordinary transfer window meant the players could move abroad for free until June 2023.
"Because of FIFA’s decision, Shakhtar has lost a chance to transfer four foreign players for the total amount of about €50 million," Shakhtar's managing director Sergei Palkin wrote in a letter to FIFA President Gianni Infantino, obtained by The Athletic.
"Everyone believes we are one football family. This decision just crossed out this slogan," Palkin told the sports website in an interview.
"We are not one football family because nobody cares about Ukrainian clubs. This is a very big pity. FIFA does not care about us."
Euronews has contacted FIFA for a response to Shakhtar's complaint. The temporary decision by football's world governing body also affected foreign players and coaches at Russian clubs.
Last week, CAS ruled that Russian teams remain barred from international football competitions, including the UEFA Champions League, over the invasion of Ukraine.
CAS noted that it was the decisions of UEFA and FIFA that had unfortunately had “such an adverse effect” on Russian football, but that it was "offset by the need for the secure and orderly conduct of football events for the rest of the world."
Russia’s exclusion means Shakhtar Donetsk keeps a place in the Champions League group stage as the team from the next highest-ranked country.
Shakhtar has not played matches in its home city in eastern Ukraine since 2014 when fighting broke out between Kyiv forces and Russian-backed separatists.
“Sport in Russia and football, in particular, serves as a major tool of state propaganda, furthering Russia’s policies of death and destruction,” Palkin said in a statement on Friday.
"We thank the court for echoing the organisations from different sectors around the world in excluding and isolating Russia from any ‘normal existence’ until it ends the war on Ukraine and relinquishes all occupied Ukrainian territories."
Shakhtar, who have won the Ukrainian Premier League 13 times, are planning to play their European games at a neutral venue in Poland next season.