The Bayern Munich head coach is now a doubt to take charge from the touchline when the German champions host Arsenal on Wednesday night, although the club had previously expressed confidence that he would be available.
Bayern confirmed Kompany's absence on Tuesday, saying: “Vincent Kompany is taking it easy due to a viral infection and will therefore miss today's training session and press conference.”
The Belgian had already been struggling during Saturday's 6-1 victory over RB Leipzig. He watched much of the match from the bench while assistant coaches Aaron Danks and René Maric took responsibility for instructions from the touchline.
Bayern sporting director Max Eberl subsequently explained that Kompany had been dealing with an infection throughout the week, alongside a hip injury that made walking difficult. He had also missed media duties after the Leipzig game.
The illness therefore comes at an awkward moment for Bayern, with Arsenal arriving for a significant Champions League fixture at the Allianz Arena. The match is scheduled for Wednesday at 9pm local time.
Danks is expected to represent Kompany at the pre-match press conference, while Bayern will monitor their head coach's condition ahead of kick-off.
There is no confirmation that Kompany will be unable to lead the team on Wednesday. Eberl had said after the Leipzig victory that the club expected the coach to be available, but his continued absence from preparations leaves some uncertainty.
Bayern will hope the 40-year-old recovers in time for a meeting between two sides expected to challenge deep into the competition. For now, his immediate priority is to rest and recover rather than take part in the final preparations.