Navalny told radio station Moscow Echo that he would have a better chance of contesting the elections, expected to be held in September, if he stood as a candidate of a party.
Current legislation requires mayoral hopefuls to either obtain 70,000 signatures backing their candidacy or be named as the representative of a registered political party.
The Kremlin-backed mayor of Moscow Sergei Sobyanin on Wednesday called snap elections two years before his mandate expires, in an apparent bid to outmanoeuvre the opposition after protests rocked the Russian capital.
Since then he has had several probes launched against him and is currently on trial for embezzlement.
Navalny has openly declared his ambition to be president and says the charges against him are a set-up aimed at wiping him off the political scene.
RPR-Parnas had previously said it was naming Navalny as its candidate, although the decision would have to be confirmed during a meeting on June 15, according to news agency Itar-Tass which quoted Boris Nemtsov, the party's co-chairman.
Sobyanin was not elected but nominated by the Kremlin in 2010 to take over from former long-serving Moscow strongman Yuri Luzhkov.
The 76-year-old Luzhkov, who was Moscow mayor from 1992 to 2010, is himself considering contesting for the post.
Other potential opponents include the liberal-inclined businessman Mikhail Prokhorov.
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