Doubts have been cast over the Armenian playmaker’s involvement in a continental clash with Chelsea on May 29.
Political tensions between his homeland and Azerbaijan have raised concerns over the impact his presence in a showpiece event could have.
Mkhitaryan was left out of Arsenal’s squad for a trip to Qarabag earlier in the season, for a group stage encounter in October, and no decision has been made as yet regarding a return to Eurasia.
The Gunners have not received the clearance they are looking for, but Tahir Taghizadeh claims their fears are unfounded.
He told Sky Sports when asked if he planned to contact Mkhitaryan: "Absolutely. I would be delighted for him to have a conversation with me.
"This is a Class A event, if our purpose is to play political games around it it is something different, you are being paid as a footballer not a politician, let's leave other issues aside.
"My message to Mkhitaryan would be: you're a footballer, you want to play football? Go to Baku, you are safe there. If you want to play the issue then that's a different story.
"What I can guarantee is that the Azerbaijan government will do everything what needs to be done and provide safety and security for every fan, player and staff member coming to this game."
Unai Emery admitted after a final day outing against Burnley in the Premier League that he has no idea whether Mkhitaryan will form part of his plans in the pursuit of major silverware.
The Arsenal manager said: "It's political issues and I don't know what the solution is.
"We want to play with every player, he worked very well [against Burnley], and we'll do all we can to play with every player and with him but I don't know the possibility [of playing] with him and the political issues.
"I don't know what the problem is between two countries but we'll do all we can to be with Mkhitaryan there.
"It's not only a sporting issue. It's not in my hands, I don't understand what the solution is."