Arsenal plan to meet with Uefa to express their fury after Henrikh Mkhitaryan decided against playing in the Europa League final over security fears.
The Armenian's safety was a concern because of the dispute between his country and Azerbaijan, the host nation of next week's fixture between the Gunners and Chelsea.
Despite receiving assurances aimed at allaying those fears, Mkhitaryan has chosen not to travel to Baku following discussions with the club and his family.
Arsenal boss Unai Emery said he respected the "personal" nature of Mkhitaryan's decision, but conceded it was "bad news" for his team.
But Arsenal managing director Vinai Venkatesham branded the situation "unacceptable" and revealed the club would make the full extent of their anger known to the governing body.
He was quoted as saying by a number of national newspapers: "I struggle to find words for how strongly I feel. We feel it's unacceptable."
Emery respects the "personal" nature of Mkhitaryan's decision not to play in the Europa League final but says it is "bad news" for ArsenalRead the full story ›
Arsenal have announced that Armenian midfielder Henrikh Mkhitaryan will not travel with the squad to the Europa League final in BakuRead the full story ›
Arsenal have revealed that Henrikh Mkhitaryan will be out for at least six weeks because of a fractured metatarsal.
Mkhitaryan suffered the injury to his right foot in last Wednesday's Carabao Cup defeat to Tottenham and was replaced at half-time before missing the win against Burnley at the weekend.
Arsenal released the news of the injury on their official website with the Armenian playmaker not due to resume full training for six weeks.
Mkhitaryan has been a regular under Unai Emery and has contributed four Premier League goals this season.
The 29-year-old will miss key league games against Liverpool, Chelsea and Manchester City as Arsenal continue their pursuit of a top-four place.
Mkhitaryan arrived at the Emirates Stadium almost a year ago as part of the swap deal that took Alexis Sanchez to Manchester United.
Doubts remain over whether Arsenal's Armenian playmaker Henrikh Mkhitaryan will travel to Azerbaijan for Thursday's Europa League Group E fixture with Qarabag.
The Gunners play at the Olympic Stadium in the capital city Baku, which will also host the tournament's final next May, but may be without Mkhitaryan due to continuing tensions between Armenia and Azerbaijan.
Hostility remains over the disputed Nagorno Karabakh region, where a ceasefire was declared in 1994 after fighting erupted several years earlier.
Those issues meant Mkhitaryan did not travel with Borussia Dortmund to a Europa League game against Gabala in October 2015, with the German club's chief executive Hans-Joachim Watzke citing "safety concerns".
There was no official confirmation from Arsenal on the matter on Monday.
After the August 31 draw, Arsenal said they would make a decision after taking to the player, signed from Manchester United in January.
Arsenal said: "Safety and security of all our players and staff is always a top priority. We will be looking into this situation, talk to the player and make a decision after that."
Henrikh Mkhitaryan's availability for Arsenal's trip to Qarabag is in doubt due to tensions between his homeland of Armenia and AzerbaijanRead the full story ›
Arsenal appeased the tension with their fans after a comfortable win over Watford at the Emirates.Read the full story ›
Henrikh Mkhitaryan insists he has nothing to prove after leaving Man Utd to join up with best friend Pierre-Emerick Aubameyang at ArsenalRead the full story ›
Arsene Wenger is concerned that Henrikh Mkhitaryan may have affected his confidence after a largely-disappointing stint at Man UnitedRead the full story ›
Henrikh Mkhitaryan has been offered no assurances over his long-term Manchester United future by Jose Mourinho.
The Armenian was one of Mourinho's first signings in the summer of 2016 but inconsistency has blighted the playmaker since he joined from Borussia Dortmund for £26.3million.
"My approach to players is that every player has a price," Mourinho said when asked directly about whether Mkhitaryan would stay.
"It doesn't matter who he is. It doesn't matter the level. It doesn't matter the prestige, the status. I think every player has a price.
"And I am not the kind of blind manager...blind in the sense of, this player is untouchable, can never be sold. I think every player has a price.
"So when the transfer window is open, it's also open for any club that is interested in our players. Then it's up to us to make the decision: yes or no. It's up to us to decide what we think is the right price.
"But Mkhitaryan played the last match in the FA Cup and probably will play the next one (against Stoke). He's a little bit the same in relation to other players that are involved in this gossip of the transfer market."