It is the second time the Russian opposition leader has been attacked with zelyonka (“brilliant green” in English) this year.
The dye is a common antiseptic in Russia and has been used in protests there and in Ukraine.
Alexei Navalny tweeted: “It looks funny but it hurts like hell.”
It is not clear who carried out the attack, which happened near the offices of the Anti-Corruption Fund (FBK) that Alexei Navalny founded.
According to a Russian report, he was diagnosed with a chemical burn to the eye.
Alexei Navalny is one of the foremost Russian critics of President Vladimir Putin and has announced his intention to run for president himself.
However, his intentions may be thwarted – he has been convicted of embezzlement, which would bar him from running for office, although he denies it.
Alexei Navalny was among 500 people arrested after organizing an anti-corruption rally last month. Rallies across Russia were the biggest opposition demonstrations in the country in several years.
He has said repeatedly that he wants to challenge President Putin’s control of the Kremlin and expose what he claims is the “myth” that Putin commands more than 80% popular support.
Meanwhile a separate opposition group, Open Russia, says its office has been raided by police, a day after the group was blacklisted by the authorities.
Activists said more than 20 riot police raided the office and removed computer equipment and 100,000 flyers for an unsanctioned rally planned for this weekend.
Open Russia was founded by former oil tycoon Mikhail Khodorkovsky, who lives in exile after spending 10 years in a Siberian prison on fraud charges, which he says were politically motivated.
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