"At 2:00 am (local time), two unidentified people sneaked into the business centre housing our editorial offices," Vladimir Todorov told AFP.
They "daubed a Celtic Cross, the number 88 and a swastika on the walls and wrote: 'You lie, Lenta'," said Todorov, 23.
The number 88 is a neo-Nazi code for the Heil Hitler salute, with 8 standing for the eighth letter of the alphabet.
They also threw a Molotov cocktail through a window but the fire was put out quickly. Noone was injured.
A Kremlin-friendly outlet, Lenta.ru is part of Rambler&Co media holding controlled by billionaire Alexander Mamut, who owns British bookstore chain Waterstones.
Moscow police said they were looking into the attack.
Todorov pointed the finger at rightwing activists, saying the website had recently published stories about skinheads as well as about cooperation between Stalin and Hitler ahead of World War II, a taboo subject in Russia.
He said Lenta.ru also wrote about members of Ukraine's far-right Azov battalion, who are battling pro-Kremlin rebels in the country's east, alleging that they sold weapons to Russian neo-Nazis.
Kremlin critics say the atmosphere of growing intolerance towards dissenters has empowered hardliners of all stripes.
Earlier this month, Molotov cocktails were hurled at the offices of film director Alexei Uchitel in protest against the upcoming release of his biopic about an affair between Tsar Nicholas II and a ballerina.
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