Steven Caulker gave Tottenham the lead by heading home a free kick in the defending champions' 2-1 victory at the Etihad Stadium on Sunday.
The problem of defending dead-ball situations has plagued Mancini's side this season but despite criticism for their zonal set-up, the Italian boss believes they would fare even worse if they changed systems.
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"If we work, we can improve the system. We have let in goals because of it, but we can change that. We are working on it, but we need to work more."
Despite their sometimes mixed form so far in 2011-12, City remain unbeaten in the Premier League and trail league leaders Manchester United by only two points.
Mancini admitted that he did not understand the concerns about his side's form so far this season, claiming that their poorer results were often a consequence of bad luck or their own mistakes.
"We have made some bad mistakes in the Champions League, have had some bad luck, and have sometimes played a bad game," he said. "But we don't have a bad problem as some people like to say."