The 32-year-old limped off early in the second half in the pre-World Cup friendly match - a terrible time for something to happen with manager Roberto Martinez to slash his preliminary squad down to 23 names in just two days.
As confirmed by the Citizens' official website, Kompany appeared to pull his groin as he stretched to make a tackle and now faces an anxious wait to see how long he'll be out for.
Kompany's injury problems have been well documented over the past few years, but in 2017/18 he played a solid handful for City as they stormed to the Premier League title.
Through careful management after missing the first third of the campaign, Kompany was able to make 17 appearances in the league.
Martinez is prepared to give Kompany some time to prove his fitness before naming his final 23-man squad on Monday. He said: "We have to look tomorrow what exactly is with Vinny.
"He felt something about his groin, tomorrow he will have a scan. Such injuries have to be rested first, but I am indeed worried.
"It's one of those setbacks that no one deserves, since he's been training here with us, he's acting on a huge level, taking responsibility and pulling the team forward, you do not want to break that kind of momentum.
"You could feel that everyone was worried when he went down. It is disappointing that you have to see Kompany leave for a scan, he knows his body and knows exactly when something is wrong."
The former Hamburg star will be desperate to feature in Russia, with Belgium under pressure to perform given their incredible squad depth.