UEFA has offered to work with Arsenal "to help find cheaper solutions" for fans to get to the Europa League final in Baku later this month.
The Gunners demanded an explanation from European football's governing body over the decision to hold the final in the capital of Azerbaijan after being allocated just 6,000 tickets for the all-Premier League clash with Chelsea.
UEFA blamed transport and infrastructure concerns for the limited allocation, with both clubs offered only a small fraction of the seats available in the 68,700-capacity Baku Olympic Stadium.
An Arsenal statement released on Thursday said it was "simply not right" for UEFA to have selected a venue that did not provide better transport options.
"We are bitterly disappointed by the fact that, due to transport limitations, UEFA can only make a maximum of 6000 tickets available to Arsenal for a stadium with a capacity of well over 60,000," the statement said.
"Time will tell if it is even possible for 6,000 Arsenal fans to attend, given how extreme the travel challenges are.
"We have 45,000 season ticket holders and for so many fans to miss out due to UEFA selecting a final venue with such limited transport provision is quite simply not right."
In a response, UEFA apologised for the difficulties fans of both finalists were experiencing. It said "experts are working on this matter with a view to help find cheaper solutions" and called for "a joint effort with your club."
"The bidding process for a club competition final is generally held a couple of years in advance, meaning that the exact circumstances in which the final will have to be organised cannot be known at the time of the appointment," UEFA said.
"The specificity of the UEFA Europa League final, when compared to the UEFA Champions League final, is the high volatility in the number of fans following the two finalist teams.
"It goes without saying that an all-English final played by two London teams was not a very predictable event at the time of the appointment. There is little doubt that this has added significant difficulties to the event logistics.
"For UEFA, fans are a priority. Football is for fans, and all of them around Europe should have the chance to enjoy unique moments of top football such as only UEFA competitions can offer. That's why UEFA would consider it utterly unfair to exclude certain venues just based on their decentralised geographical position."
Fans of both Arsenal and Chelsea hit out at the decision to stage the final in Baku, which has left those who can afford to travel and are able to get tickets with a 2,850-mile trip.
There are no direct flights to the city in the week of the final, meaning fans facing 25-hour journeys and stopovers in Frankfurt, Vienna, Kiev, Istanbul and Tehran. The Foreign Office has also warned that terror attacks in Baku are "likely."
Meanwhile, Arsenal forward Henrikh Mkhitaryan has been assured that he will be able to travel to Baku despite tensions between his native Armenia and neighbouring Azerbaijan.
Mkhitaryan has previously avoided travelling to Azerbaijan and was not part of the Arsenal squad when they played Qarabag in the Europa League group stage in October.
Last week, a spokesperson for the Azerbaijan Foreign ministry said the country had hosted many sporting events in which Armenian athletes had taken part.