WeChat, which had 889 million global users by the end of 2016, was not properly registered with Russian regulators, Tencent said.
It is not clear how many Russia-based users the app has.
"We're experiencing a block and we're deeply sorry," a company official said on a Tencent microblog.
"Russian regulations say online service providers have to register with the government but WeChat doesn't have the same understanding (of the rules)," the official added.
However, Chinese state news agency Xinhua quoted a spokesman for Russia's telecommunication watchdog as saying WeChat "did not provide the contact information necessary for registration with authorities".
A law passed in 2014 requires foreign messaging services, search engines and social networking sites to store the personal data of Russian users inside Russia.
Sites that breach the law are added to a blacklist and internet providers are obliged to block access.
The law prompted criticism from internet companies but entered into force in September 2015, with professional networking site LinkedIn blocked after it was found to have broken the law.
WeChat, known as Weixin in China, is more than just a messaging app.
It offers payment, ride-hailing and other services and Tencent has ambitions to spread it far beyond its home country.
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