The warning comes a day after Dmitry Muratov spoke to Ukrainian President Volodymyr Zelenskiy in a group interview with Russian journalists that was quickly banned by the state media watchdog Roskomnadzor (RKN).
"We suspend the publication of the newspaper on our website, in social networks and in print media until the end of the 'special operation on the territory of Ukraine," the newspaper wrote on its website. Muratov said the decision was difficult but necessary: "There is no other option.... For us, and I know for you, it is a horrible and difficult decision".
Novaya Gazeta is one of the country's leading independent newspapers. Six of its journalists, including Anna Politkovskaya, have been killed since the 1990s for their reporting.
Novaya Gazeta's announcement follows the closure of radio station Ekho Moskvy and TV Dozhd.
On Monday 28th March, the Russian Justice Ministry added Germany's Deutsche Welle to a list of media outlets it has labelled "foreign agents".
“The Kremlin is trying to cover up the Russian army’s war crimes in Ukraine by all means,” said EFJ General Secretary Ricardo Gutiérrez.
IFJ General secretary Anthony Bellanger said: "Attempts to cover up the devastating impact of Russia's war in Ukraine are preventing independent media from doing their job in Russia. Novaya Gazeta's decision is an acknowledgement of the impossiblity for independent media to report on the situation without fear of prosecution. Above all, during times of conflict, it is vital the public has the right to know. We urge the Russian government to stop targeting the media and let journalists carry out their jobs freely".