He had served in the Russian army during the two wars in Chechnya in 1990s and became one of Russia's best-known war reporters.
Ukrainian authorities released a drawing of the man they suspect is Mr Babchenko's assassin, about 40-45 years old, with a grey beard and wearing a cap.
But in Moscow, Russia's Investigative Committee distanced the Kremlin from the killing - saying it had launched its own criminal investigation into Babchenko's death.
Russian foreign minister says his country's secret services had nothing to do with the killing of Arkady Babchenko.
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I feel so empowered by @iamwandasykes, Channing Dungey and anyone at ABC standing up for morals and abuse of power. Barr also apologized to Jarrett in a later tweet, with the actress "very sorry" about the hurt caused.
Anton Gerashchenko, a Ukrainian lawmaker and an adviser to the country's interior minister, said that the investigaion would look at "Russian spy agencies' efforts to get rid of those who are trying to tell the truth about what is going on in Russia and Ukraine", The Guardian reported. The incident killed all 92 passengers on board, including the members of a renowned Russian military choir and several staffers for state news agencies.
Babchenko had grown highly critical of the Russian government in recent years.
"My home address has also been published on the internet, together with an invitation 'to visit.' I have received threats to me and my family by the thousand - in my email inbox, on Facebook and by phone", he wrote.
Ukraine's Security Service suggested it had staged the murder.
A number of Novaya Gazeta journalists have been killed, including Anna Politkovskaya, who was gunned down in the stairwell of her Moscow apartment in 2006. Some called for Babchenko to be stripped of his Russian citizenship.
"I used to be a good soldier", Babchenko wrote in 2017.