The commission will meet "soon" to discuss violations in the campaign of the leader of the country's protest movement, its chief Valentin Gorbunov said.
"If the violations exceed the norms established by the law than the question will be raised of cancelling the registration of the candidate," Gorbunov said in comments confirmed to AFP by a spokesman.
The election commission later said, citing "multiple" voters' reports, that the violations included the distribution of campaign literature.
"Oi! The Moscow election commission announced that I could be removed from the polls," Navalny said in a message on Twitter.
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"Opinion polls show that I have every chance to get into a second round and win," Navalny added on Echo of Moscow radio. "They will do everything to stop this scenario."
Pro-Kremlin Moscow mayor Sergei Sobyanin is widely expected to win the poll but Navalny has vowed to force it into a runoff, which would happen if Sobyanin failed to win 50 per cent of votes in the first round.
Pro-Kremlin VTsIOm pollster puts election ratings for Navalny at 13-15 per cent.
Support for Navalny has risen from s ingle digits just a month ago as Navalny launched a robust Western-style campaign complete with fiery stump speeches and eye-catching paraphernalia.
He was allowed to run for mayor in a hugely surprising move after a court sentenced him to five years in prison last month for embezzlement in a disputed verdict.