The prominent Russian war correspondent and former soldier was shot dead on Tuesday evening in an apparent contract-style killing in the stairwell of his building in Kiev. He had moved to the Ukrainian capital last year following a campaign of harassment in Moscow.
The 41-year-old was the latest in a number of Kremlin critics to have been killed in Kiev in the past two years.
Ukrainian police have opened a murder probe, saying they suspect the crime was linked to his work.
“I am convinced that the Russian totalitarian machine did not forgive him his honesty and principled stance,” Ukrainian Prime Minister Volodymyr Groysman said Tuesday.
“A true friend of Ukraine who was telling the world the truth about Russian aggression. His murderers should be punished.”
An aide to the Ukrainian interior minister, Anton Gerashchenko, also pointed the finger at Moscow, writing on Facebook: “The Putin regime targets those it cannot break or intimidate.”
Many politicians and observers including Foreign Minister Pavlo Klimkin suggested Russia wanted to sow chaos in the country – already wracked by a four-year conflict with pro-Russian rebels in the east – ahead of presidential and parliamentary elections next year.
“The leading and obvious line of inquiry is that of his professional activities,” said Kiev police chief Andriy Kryshchenko.
Ties between Russia and Ukraine were shredded after a popular uprising ousted a Kremlin-backed president in Kiev in 2014 and Russia annexed Crimea and moved to support insurgents in the east of the former Soviet state.
Moscow denied being behind the killing.
“The Ukrainian prime minister is already talking about how it was done by Russian secret services,” Foreign Minister Sergei Lavrov told reporters. “This fashion of conducting international affairs is very sad.”
Kremlin spokesman Dmitry Peskov said: “We strongly condemn this killing and hope for a real, and not a sham investigation into determining who ordered it.”
Investigators in Moscow opened their own probe, saying they were “not going to turn a blind eye to the cruel crimes against Russian citizens”.
Ukrainian police spokesman Yaroslav Trakalo said Babchenko was found bleeding by his wife after she heard shooting, and that he died in an ambulance en route to hospital.
The journalist suffered three gunshots to his back.
His murder was reminiscent of the assassination of several prominent Kremlin critics including politician Boris Nemtsov who was gunned down near the Kremlin in 2015 and journalist Anna Politkovskaya who was shot and killed in the stairwell of her Moscow apartment in 2006.
Several have also been killed in Ukraine in recent years, with one gunned down on a Kiev street in broad daylight and another whose car exploded.
Several countries condemned the Babchenko killing, with British Foreign Secretary Boris Johnson saying he was “appalled”.
“We must defend freedom of speech and it is vital that those responsible are now held to account,” he said on Twitter.
The Council of Europe also condemned the “brutal act”, with Secretary General Thorbjorn Jagland saying: “It must be fully investigated and the perpetrators quickly brought to justice.”
Babchenko fought in Russia’s two Chechen campaigns in the 1990s and early 2000s before becoming a war correspondent and author. He repeatedly said he faced death threats.
He contributed to a number of media outlets including top opposition newspaper Novaya Gazeta and was an avid blogger, accusing Russian authorities of killing Kremlin critics and unleashing wars in Ukraine, Syria and elsewhere.
He wrote about his experience as a young soldier in the Chechen campaigns in a book published in English under the title “One Soldier’s War”.
Babchenko left Russia in February 2017 after receiving threats, living first in the Czech Republic, then in Israel, before moving to Kiev.
He had hosted a programme on the Crimean Tatar TV station ATR for the past year.
Babchenko had made a name for himself with his poignant reportages from the frontlines, including the conflict in eastern Ukraine that has killed more than 10,000 people.
In recent years his increasingly bombastic posts constantly pushed the boundaries of good taste and some of his colleagues and followers stopped reading him on Facebook.
But his killing triggered an outpouring of grief among liberal Russians.
A group of around 30 people, mostly journalists, gathered at the Russian embassy in Kiev, hanging a picture of Babchenko on the wall and leaving flowers.
Vigils were being planned in Russia and Ukraine.
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