Vasyl Gritsak, head of the Ukrainian Security Service, announced at a news conference Wednesday that the security agency and the police had solved Babchenko's slaying.
Kiev and national police had said Babchenko, a strong critic of the Kremlin, was shot multiple times in the back at his apartment building and found bleeding by his wife.
Babchenko, one of Russia's best-known war reporters, fled the country in February 2017 after receiving death threats.
Russia had demanded on Tuesday that Ukraine conduct a full investigation into his death, though many suspected that Russians were behind it.
Anton Gerashchenko, a Ukrainian MP who serves as an adviser to the interior minister, said on Facebook that investigators would be looking 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".
Russian journalist Arkady Babchenko, a prominent critic of President Vladimir Putin and the Kremlin, was shot dead on Tuesday in Ukraine's capital city.
Harlem Desir, the media freedom representative at the Organization for Security and Co-operation in Europe, said he was "horrified" by Babchenko's death. Prominent Russians to have been murdered in Kiev include journalist Pavel Sheremet, who was killed in a auto bomb in 2016, and ex-Russian lawmaker Denis Voronenkov, who was shot dead in 2017. "Now, for the most part, the people that Russians hate-it's all of you". He left Russian Federation in February 2017 because he feared for his life, according to Reuters.
He moved to Kiev, where he worked for a Crimean television station and produced coverage critical of Russia's military actions in Ukraine.