The man, who sustained a gunshot wound, was found in his own apartment by his wife, who called the emergency services, the police said.
However, Muzhdabaev said that Babchenko did not report on Ukrainian affairs and that his journalism was exclusively "about the Russian government, about their actions, about their criminal activities, that's all".
The Ukrainian security service had orchestrated the death fake-out in an effort to apprehend those who were already actively trying to murder Babchenko.
"According to information received by the Ukrainian security service, the killing of Russian journalist Arkady Babchenko was ordered by the Russian security services themselves", Vasyl Hrytsak, head of the Security Service of Ukraine (SBU), told the news conference before adding that his slaying had been solved.
Arkady Babchenko died from his injuries on the way to the hospital after being shot in the back near the entrance to his Kiev apartment, Ukrainian law enforcement said on social media.
"Olechka, I am sorry, but there were no options here", Babchenko declared.
"I apologize to my wife".
Mr Babchenko told the news conference he'd previously fled Russian Federation after receiving death threats.More news: Donald Trump's Russian Federation claim contradicts, um, Donald Trump's Russian Federation claim
Ilya Ponomarev, a former Russian lawmaker who also moved to Ukraine, said Mr Babchenko continued to be threatened after he settled past year in Kiev, where he worked as a host for the Crimean Tatar TV station.
Several Russian journalists and other dissidents have been killed in recent years in Kiev. The 41-year-old, who fought with the Russian army in Chechnya in the 1990s and went on to cover conflicts in Georgia's breakaway region of South Ossetia and Ukraine, had previously faced a campaign of harassment over his reporting. He was given $40,000 to organize the murder, $30,000 for the killer and $10,000 for being an intermediary, the SBU said.
In both cases, Ukraine's government blamed Russian Federation for being involved.
In a Facebook post hours before the fake killing, Babchenko wrote about his "second birthday" when a Ukrainian general refused to let him on a helicopter that was then shot down by Kremlin-backed rebels, killing 14 people on board in 2014.
Ukrainian officials led by Prime Minister Volodymyr Groysman had accused Russian Federation of being behind the killing of the Kremlin critic, a charge that Moscow batted back.
"I'm still alive", he said.
Babchenko was well-known for his criticism of the Kremlin.
Media outlets around the world, including Newsweek, covered the "murder", as foreign and Ukrainian officials voiced their suspicions that Moscow was behind the journalist's death.