Vasyl Gritsak, the head of the Ukrainian Security Service, announced at a news conference that the security agency and the police had solved Mr Babchenko's killing.
"Some called for me to be stripped of citizenship, others are making an online game where you can beat me to death", he said.
He said a Ukrainian citizen had been recruited by the Russian security service and paid $40,000 to organise the murder of the journalist.
Ukraine's chief of security services, Vasyl Gritsak, said Ukrainian police had detained one suspect involved in the real plot against Babchenko, a former rebel fighter in eastern Ukraine - in other words, one allied with Russian Federation in the fighting there.
"I would like to apologize for what you have all had to go through", Babchenko told reporters.
"The first version is his professional activity", said Kiev police chief Andriy Kryshchenko on the TV news channel 112, when asked what police suspected lay behind the murder.
Babchenko, a former soldier in the Chechen war who became one of Russia's best-known war correspondents, had left his homeland fearing for his life after criticising Russian policy on Ukraine and Syria.More news: Top North Korean official holds talks in New York
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"Reporters Without Borders (RSF) condemns the distressing simulation of Russian exile journalist Arkady Babchenko's murder", Reporters Without Borders said today in a press release.
Grytsak also thanked Babchenko and his family, who he said were in the loop about the secret operation.
But on Wednesday, Babchenko appeared before reporters saying he had been part of a special Ukrainian operation to stop a Russian attempt on his life.
Kremlin critic Arkady Babchenko has been seen in Ukraine.
Mr Gerashchenko said Mr Babchenko's killer was waiting for him on the staircase inside the journalist's building and shot him in the back as he was going out to buy bread.
Prominent Russian journalist Arkady Babchenko.
Russian Federation said it was happy that Mr Bachenko was alive after all.
Babchenko sparked a backlash in Russia for his comments in a 2016 Facebook post on a Russian military plane crash. Babchenko had left Russian Federation for Ukraine in February 2017 because he feared for his life.