The 48-year-old has criticised Marc Wilmosts for failing to 'understand the situation' surrounding the City captain's injury problems
The defender has been sidelined since January when he suffered a calf injury in the FA Cup fourth-round win over Stoke, with the Italian recently revealing he was due to return in City's clash with Newcastle on March 30.
However, the Belgian started and played the full 90 minutes of his country's 1-0 win on Tuesday, leaving his club boss furious at a perceived lack of understanding from Wilmots.
"I don't agree with this," he told reporters. "International managers should understand the situation.
"He didn't play for us for 60 days, but he goes and plays for [Belgium]."
Mancini conceded defeat in the Premier League title race on Friday, admitting that the 15-point gap to leaders Manchester United is too much for his side to make up in the remaining matches.