The City skipper, 30, is currently on international duty with Belgium and had been set to start against Holland in their friendly match in Amsterdam on Wednesday night.
Kompany was named in Roberto Martinez’s original starting XI when the teamsheet was handed in before kickoff.
But 30 minutes later, Kompany had withdrawn from the action, replaced by Christian Kabasele.
Officially, the line from the Belgian camp is that Kompany did not suffer a recurrence of his recent groin problems but rather pulled himself out as a preventative measure.
They insist he will be fine to face Estonia on Sunday.
But it is yet another worry for the City captain, and his club manager, Pep Guardiola.
The Spaniard may have viable alternatives to the 30-year-old on the pitch from a positional standpoint but Kompany remains crucial with his experience and leadership.
However, he has played just 78 minutes in the Premier League since re-injuring his groin – on his return from a six-month absence – at Swansea in September.
And he has only been on the bench for City’s last two matches.