Logistical difficulties in reaching Baku, the venue for the all-English final between Arsenal and Chelsea on May 29, have led to fans being given an allocation of just 12,000 tickets - 6,000 for each team.
Speaking last week, Klopp bemoaned the location of the European showpiece, saying: "These guys who make the decisions, I don't know what they have for breakfast really when they do it."
But general secretary Elkhan Mammadov of the Azerbaijan FA responded: "I was unpleasantly surprised by the remarks of Jurgen Klopp,' he said. 'He always gave an impression of a very positive person. Moreover, we all know that he is a great specialist who has achieved really outstanding results in football.
"But with all this, I strongly disagree with his opinion that football should be geographically limited.
"We must respect and promote the values of football. And one of our main values is the expansion of the boundaries of football and its globalisation.
"Europe has long gone beyond the borders of the countries of the western part of this continent.
"And I am convinced that holding European Championship matches and European Cup finals in Eastern Europe opens up new opportunities for developing football in these countries, serves to make it more popular among the younger generation, attracts young people to football.
"The same can be said about the organisation of the Champions League final in Kiev or 10 years ago in Istanbul.
"Yes, perhaps this year the prices in Madrid have risen because of the Champions League final, but this is the so-called side effect of a market economy and it happens everywhere on the eve of big sporting events.
"I agree that getting to Baku by bus from London will be difficult, but [since] when was the distance a barrier for real fans?
"I want to remind you that three cities participated in the tender for the final: Seville, Istanbul and Baku. No one limited the ability of other countries to participate.
"I am sure that there will be a real football holiday in Baku. And I am also confident that the same will happen in Madrid."