Speaking at the press conference, the head of Ukraine's security services, Vasyl Hrytsak, confirmed the journalist was alive.
You can receive Breaking News on a smartphone or tablet via the BBC News App. He accused Ukraine and its "Western handlers" of seeking to use it to stir up anti-Russian feeling, saying it followed a familiar pattern of using such assassinations to frame Russia.
Babchenko served as a soldier in both wars in Chechnya before turning his bleak experience into the acclaimed memoir One Soldier's War.
Before ushering Babchenko into the room, Gritsak said investigators had identified a Ukrainian citizen who had been recruited and paid $40,000 by the Russian security service to organize and carry out the killing.
"Arkasha would shoot straight from the hip every day in such a brazen manner that even those close to him felt uneasy sometimes", wrote Pavel Kanygin, a journalist for Novaya Gazeta, referring to his friend by his nickname.
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Babchenko was one of Russia's best-known war correspondents, and had reported multiple times from the war-torn Donbas region in Ukraine, Kyiv Post reported.
Police said they believe Babchenko was likely targeted because of his work.
A top lawmaker says Russia is willing to help Ukraine investigate the murder of a Russian journalist.
His criticisms attracted the fury of pro-Kremlin officials and activists, as well as state media, and for years he endured regular abuse and threats.
Ukrainian Prime Minister Volodymyr Groysman, in comments posted to his Facebook page, also implied involvement by Putin's government in Babchenko's death.
Babchenko was widely respected in Russian Federation and Ukraine's journalistic communities as an unblinking and remarkably talented chronicler of war. He then he became a war reporter for several Russian newspapers. "The organizer was talking about killing another 30 people in Ukraine".
"I was lucky. A second birthday, it turns out", Mr Babchenko wrote.
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