Roskomnadzor's warning to Ekho Moskvy related to this week's program, in which two journalists exchanged first-hand accounts of fighting between pro-Russia rebels and government forces in eastern Ukraine.
The journalists, Sergei Loiko of the Los Angeles Times and Timur Olevskiy of Russia's independent Dozhd television station, talked, in particular, about fighting around the airport in the main rebel-held city of Donetsk, that has continued despite a truce signed in September.
The agency said Friday the program contained "information justifying war crimes," but didn't elaborate.
Under Russian law, a media outlet could face closure if it receives two warnings in one year. The warning was the first for Ekho Moskvy.
While most Russian media toe the government's line, Ekho Moskvy has given a platform to Kremlin critics despite being majority-owned by a branch of Gazprom, Russia's state-controlled gas giant.
Media freedom in Russia has steadily shrunk under the rule of President Vladimir Putin. With all nationwide television stations under state control and most print media full of adulation for Putin, authorities have methodically moved to tame few remaining independent media outlets amid a strain with the West over Ukraine.
And last month, Russian lawmakers approved a bill that would limit foreign ownership in Russian media to 20 percent. The measure was widely seen as directed at critical print outlets with foreign ownership, such as the Vedomosti business daily and the Russian Forbes magazine.