The messaging app claims that Moscow is trying to push users towards its own state-sponsored communications app, Max, although it did not disclose any details on what action was taken to block the app or to what extent it was successful.
A WhatsApp spokesperson told The Guardian newspaper: "Trying to isolate over 100 million users from private and secure communication is a backwards step and can only lead to less safety for people in Russia. We continue to do everything we can to keep users connected."
The move fits into Russia's plans to achieve a "sovereign internet" - an online space that is cut off from Western technology and foreign influence and is susceptible to state control.
The latest row between the Kremlin and WhatsApp comes amid a wider crackdown on social media that recently targeted Telegram - another messaging app that is used by over 60 million Russians per day.
The decision triggered a backlash from Russian troops on the frontline in the war with Ukraine, as well as pro-war bloggers and opposition figures in exile.
As users reported slower traffic and download delays earlier this week, Telegram's Russian-born founder Pavel Durov - who is based in Dubai - hit out at the Russian authorities.
He said: "Restricting citizens’ freedom is never the right answer.
"Telegram stands for freedom of speech and privacy, no matter the pressure."
Max is modelled on China's "super app" WeChat and is used by approximately 55 million users in Russia.
Last August, Moscow ordered Max to be pre-installed on new phones and dismissed critical claims that the app could be used to spy on users.
When asked if WhatsApp would return in Russia, Kremlin spokesperson Dmitry Peskov told Russian news agency Tass: "This is again a question of fulfilling the legislation. If the Meta corporation fulfils this and enters into dialogue with Russian authorities, then we have the possibility of reaching an agreement."
He added: "If the corporation [Meta] sticks to an uncompromising position and, I would say, shows itself unready to align with Russian legislation, then there is no chance."
