Arsenal manager Unai Emery said Armenian midfielder Henrikh Mkhitaryan's decision to miss the Europa League final against Chelsea in Baku was a "personal" one amid fears over his safety.
Mkhitaryan's well-being was a concern for Arsenal due to the tense political dispute between Armenia and final hosts Azerbaijan.
The Premier League club have decided against Mkhitaryan travelling with the rest of Emery's squad for the game on May 29.
"It's bad news, but we cannot do anything for this issue," said Emery.
"I spoke this morning with Mkhitaryan. It's a very personal decision. He wants to play and to help us, but they spoke, both family and him, and decided to not go... I cannot push him to come with us."
Arsenal said all options had been explored to guarantee the midfielder's safety.
"We are very disappointed to announce that Henrikh Mkhitaryan will not be travelling with the squad for our UEFA Europa League final against Chelsea," an Arsenal statement announced on Tuesday.
"We have thoroughly explored all the options for Micki to be part of the squad but after discussing this with Micki and his family we have collectively agreed he will not be in our travelling party."
Azerbaijan's foreign ministry spokeswoman, Leyla Abdullayeva, told AFP that "in spite of the difficult relations between Azerbaijan and Armenia, Mkhitaryan can play in the Europa League final in Baku".
"Armenian sports figures have already taken part in numerous major sporting events that Azerbaijan has welcomed previously. One shouldn't mix up sport and politics," she said.
- Tough decision -
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But Mkhitaryan had earlier tweeted: "Having considered all the current options, we had to take the tough decision for me not to travel with the squad to the UEL Final against Chelsea.
"It's the kind of game that doesn't come along very often for us players and I must admit, it hurts me a lot to miss it. I will be cheering my teammates on! Let's bring it home."
UEFA, European football's governing body, insisted they had done all they could to ensure Mkhitaryan's safety in Baku.
"Working alongside Arsenal FC, UEFA sought and received assurances regarding the player's safety in Azerbaijan from the highest authorities in the country," a UEFA statement read.
"As a result of these guarantees, a comprehensive security plan was developed and given to the club.
"While the club acknowledges the efforts that UEFA and the Azeri government have gone to in this matter, we respect the personal decision not to travel with the player."
Mkhitaryan had featured in 11 games during the Europa League campaign and his absence will be a big blow as Arsenal look for the victory they need to qualify for next season's Champions League.
Arsenal have also expressed their displeasure at the selection of Baku as host city for the game given the logistical problems and huge cost faced by fans for a near 5,000 mile round trip from London.
"We have written to UEFA expressing our deep concerns about this situation," the Arsenal statement added.
"We're also very sad that a player will miss out on a major European final in circumstances such as this, as it is something that comes along very rarely in a footballer's career.
"Micki has been a key player in our run to the final so this is a big loss for us from a team perspective." Armenia captain Mkhitaryan skipped the Gunners' Europa League fixture against Qarabag in October because of tensions caused by a dispute over the Nagorny Karabakh region.
Azerbaijan and Armenia have feuded over Nagorny Karabakh since Armenian separatists seized the territory in a war that claimed about 30,000 lives in the early 1990s.
A ceasefire was agreed in 1994 but the two countries remain locked in a bitter dispute with frequent exchanges of fire, and tensions are such that Mkhitaryan also did not travel to Azerbaijan with former club Borussia Dortmund for a Europa League match against Galaba FK in 2015.
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