Balotelli, who has started just six out of 14 league games in this campaign, broke the deadlock on 69 minutes at the DW Stadium as unbeaten City won 2-0 to stay a point behind leaders Manchester United.
The striker, who bagged 13 league goals last season to help fire City to the title, followed up to score at the second attempt after his first shot was blocked by Wigan keeper Ali-Al-Habsi, who had allowed him the chance after failing to hold Gareth Barry's low strike.
Mancini, though, opted not to dip into his bag of platitudes.
"I think Mario can do better. He scored one important goal but can continue to improve," he told reporters.
"For me, he did not play very well."
Earlier this month Mancini said the striker, who scored two superb goals for Italy in their Euro 2012 semi-final defeat of Germany, could become one of the best players in the world.
"He could be like Cristiano Ronaldo or Lionel Messi if he worked harder in training."
Balotelli's only other two goals for City this season came in the League Cup and Champions League.
City's win came at a cost with James Milner, who scored a fine second goal, picking up a hamstring injury.
"I was happy for James but it was a second hamstring injury for him and I hope he'll be back in 10 days," Mancini said.
