During the press conference, reporters were told that the staging of Babchenko's death had been coordinated by the journalist and Ukrainian police following serious death threats against him.
A day earlier it was reported that he had been shot dead at the door of his apartment in Kiev - with numerous commenters in Ukraine blaming Russian Federation for the crime.
A prominent Russian journalist and critic of President Vladimir Putin was shot dead in Ukraine where he had fled into exile following threats, police said on Tuesday. "Special apologies to my wife".
Mr Babchenko, one of Russia's best-known war reporters, spoke and wrote previous year about leaving the country because of repeated threats that he and his family would be harmed.
Arkady Babchenko, who moved to the city past year following threats in his homeland, was sacked on after returning from buying bread and died of his injuries in an ambulance, local police said late Tuesday.
"Some called for me to be stripped of citizenship, others are making an online game where you can beat me to death", he said.
In response to allegations that Moscow may have been the murder, Matviyenko said "Russia had no motivation" to kill the journalist, the state-run TASS news agency reported. They said the killing may relate to his work.
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Police said he had multiple gunshot wounds on his back.
The SBU also said that the assassin was apprehended, and that Russian intelligence had paid the assassin $30,000 thousand for the hit.
Babchenko was an outspoken critic of the Kremlin, speaking out against Russia's annexation of Crimea and against Russian involvement in Syria. I believe it to be a personal attack by Babchenko against our media community.
Some even called for stripping Babchenko of his Russian citizenship.
In a controversial 2016 Facebook post, Babchenko wrote he had "no sympathy or pity" for the victims of a plane crash carrying Russia's Red Army choir to Syria given Moscow's support for Bashar al-Assad.
In early 2017, after spending years fearing he would be arrested, beaten, or worse, Babchenko left Russian Federation. "In Russia, dissidents like me are harassed with impunity".
A former war correspondent, he worked in Kiev as a presenter on Ukraine's channel ATR TV.
Babchenko was 19 when he was sent to fight in Russia's first Chechen campaign in the 1990s as a conscript.