The decision comes amid a spike in violence against dissenters in Russia, including this week's attack on a radio journalist who was stabbed in the neck at the offices of the liberal Echo of Moscow radio.
"If the state is not ready to protect us, we will protect ourselves," Sergei Sokolov, a deputy editor at Russia's top opposition newspaper, told AFP today.
"When journalists find themselves helpless in the face of lawlessness in the streets and indiscipline of law enforcement agencies there is no other way."
The use of fire arms is tightly regulated in Russia. The so-called traumatic weapons that use rubber bullets can be used for self-defence but can also inflict lethal damage.
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"I will arm the newsroom," Muratpv said on Echo of Moscow radio.
"We will also supply journalists with other security means that I don't want to talk about."
"We will conclude an official agreement with the Russian interior ministry," he added. "I have no other choice."
Contacted by AFP, Muratov said he could not provide details of the plan over security concerns.
Pavel Kanygin, a Novaya Gazeta special correspondent, said he was ready to use non-lethal weapons to defend himself.
"I don't see anything bad in our situation," he told AFP in written comments, adding that potential criminals may be deterred by the knowledge that Novaya Gazeta reporters carry weapons.
"This too is defence."
President Vladimir Putin's spokesman said today he saw no reason to provide extra security for journalists.
"Unfortunately, everyone of us can become a target of a madman," Dmitry Peskov told reporters, adding Novaya Gazeta was free to adopt any measures as long as they were in line with existing laws.
Earlier this week Tatyana Felgenhauer, a 32-year-old Echo of Moscow presener, was stabbed in the neck by a mentally unstable man.
Many commentators have blamed the authorities for fomenting hatred against dissenters and creating an atmosphere in which such attacks became possible.
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