Ukrainian police said Voronenkov was shot dead by an unidentified gunman near the entrance of an upscale hotel in the Ukrainian capital. Both the assailant and the bodyguard were taken to the hospital, the Kyiv Post reported citing police.
Voronenkov and Ponomarev are among Russian dissidents who Ukrainian political analyst Volodymyr Fesenko said have fled Putin's authoritative regime since the annexation of Crimea.
Kremlin spokesman Dmitry Peskov swiftly dismissed Kiev's accusations as "absurd" in comments to Russian news agencies, adding that Moscow "hopes that the killer and those behind him will be found". "Yes, I confirm that he is Denis Voronenkov", Krishchenko said.
Denis Voronenkov left Russian Federation after saying he was persecuted by security agencies.
After leaving Russian Federation, he became openly critical of Moscow's annexation of Crimea in 2014, testifying in a case against Ukraine's former pro-Russia president Viktor Yanukovych, who was ousted earlier that year.
He was a critic of Russia's annexation of Crimea in 2014 - despite voting in favor of it at the time - and he repeatedly criticized Putin after his defection.
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Voronenkov, 45, was an ex-member of the communist faction in the lower house of the Russian parliament.
Television footage showed Mr Ponomarev and Ms Maksakova leaving the scene in a auto together with Ukraine's General Prosecutor Yuriy Lutsenko. Maria Maksakova, an opera singer who also served in the Duma, moved to Ukraine with her husband past year.
Russian investigators have filed fraud charges against him in connection with his business activities after his move to Ukraine.
"There's an obvious theory - I've said that Voronenkov wasn't a crook, but a deadly unsafe investigator for Russian officials", Ponomarev wrote on Facebook.
"Now, though, Voronenkov appears to have flipped, becoming a fiery critic of most everything he once supported in Russian Federation and a citizen of Ukraine, to boot". An anonymous Russian law enforcement officer was quoted as saying there was no "criminal element" involved, but the timing - that he "fell" a day before he was to testify in the Moscow City Appeals Court against another court's decision not to reinvestigate the corruption case for which Magnitsky died - is, to say the least, suspicious. Tensions have been running high since Russian Federation invaded Crimea in February 2014. The president of Ukraine is calling the killing a "Russian act of terrorism". "This was a typical show execution of a witness by the Kremlin", Mr Lutsenko said.
"There's an obvious theory - I've said that Voronenkov wasn't a crook, but a deadly unsafe investigator for Russian officials", Mr Ponomarev wrote on Facebook.