Kompany made his first competitive appearance in eight weeks when he featured in his country's World Cup qualifier against Macedonia on Tuesday.
The 26-year-old defender had been sidelined since suffering a calf injury in the FA Cup fourth-round win at Stoke on January 26 and had a potential comeback date put back several times.
That did not prevent him being called up by Belgium and although the national skipper did not play in last Friday's game in Macedonia, he played all 90 minutes of the return fixture in Brussels.
Mancini said: "He didn't play for us for 60 days and then he went to play for the Belgium team.
"I did not agree with this. I think sometimes some managers of national teams should understand the situation.
"This player plays for the club and the club, every month, pay his salary.
"I don't know if he is okay or not. One week before the international break he was not fit to play for us.
"I didn't see Vinny yesterday [Wednesday]. I will see him today [Thursday]."
Mancini hopes Kompany will be fit to return for his side in Saturday's Barclays Premier League clash with Newcastle at the Etihad Stadium.
Mancini, speaking at a press conference to preview the game, added that striker Sergio Aguero is fit and could make his comeback.
The 24-year-old has missed City's last three games with a knee injury.
He returned to Argentina for treatment during his lay-off, and linked up with the national squad, but did not play and has been back training at Carrington for the past week.
Mancini said: "Sergio is okay. I think he could be ready for Saturday."