The disappointed midfielder was told his club’s needs were greater than his country’s, even though neighbours Brentford gave Lasse Vibe permission to join Denmark.
Christensen came on as a 69th minute sub in the 1-0 win over Newcastle on opening night, and played all 90 minutes plus in the 3-2 win at Leyton Orient on Tuesday to underline Joka’s point.
"It was my decision as our squad is very short," Jokanovic said.
"I understand it is the Olympic Games and it is a very nice opportunity for the old sportsmen and it can be one time in the life, but he is a football player.
"At the end of the month all of us is waiting for a wage and our obligation is working here in Fulham.
"Fortunately, the Olympics is not in the international days where I am obligated to send people for their national team.
"From one side I understand he can be a little bit unhappy, but he can understand where he is and our first choice is Fulham.
"I can decide I want to be in different places in different moments. But my obligation is to be here and be ready because I am a professional coach like he is a professional football player."