Navalny accused authorities of creating yet another hurdle for his campaign for the 2018 presidential elections, announced last month.
Yandex Money said: "The law requires us to limit use of digital wallets for goals and methods that could be viewed ambiguously in terms of law... We have to minimise these risks.
"We have decided to change the client agreement to add the clause that limits collection of funds into a wallet for political goals," it said in a statement, calling the measure "standard for the industry".
The charismatic politician has regularly used the internet to rally support and funded most of his Moscow mayoral campaign in 2013 through individual online donations, although he lost the race to the incumbent pro-Kremlin mayor.
He was the first person to declare himself a candidate for the next presidential polls, in which President Vladimir Putin is also expected to run.
In a blog post Monday, Navalny wrote that his contacts in Yandex Money have reported being pressured by the Central Bank to "use any pretext to close the online wallet" used for Navalny's campaign.
Navalny slammed such pressure as a "crime" by the Central Bank employees and sent a letter to bank chief Elvira Nabiullina demanding an end to such pressure which "inhibits the public campaign regarding my presidential bid".
Yandex Money was founded by Yandex, the sprawling internet giant that owns Russia's most popular search engine. It now controls a 25 per cent stake in the payment system while the rest is owned by Sberbank.
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