Bogdan Tyvodar of the Ukrainian security service told journalists an unnamed Ukrainian citizen had been arrested after being sent from Russia to commit a series of "terrorist acts" in the neighbouring country.
The Ukrainian security service also said Friday it was seeking another alleged organiser of the planned murder, Ukrainian citizen Vyacheslav Pivovarnik, who they say is currently on the run in Russia.
Anti-Kremlin journalist Babchenko made a scarcely credible reappearance at a press conference in Kiev last month less than 24 hours after the Ukrainian authorities reported he had been shot dead at his home in a contract-style killing.
Kiev came under fire after it admitted to staging the murder, though it claimed it was the only way to prevent a real assassination.
Another Ukrainian, Boris German, was arrested on May 31 on suspicion of organising the attempted murder, after allegedly being recruited by Russian secret services.
Oleksiy Tsymbaliuk, a former Ukrainian Orthodox priest who fought against pro-Russian separatists in Ukraine's east, told the BBC he had been approached by German and offered money to kill Babchenko.
Tsymbaliuk said he tipped off the Ukrainian security services.
German, a weapons manufacturer, said that he was working with the country's security services and knew from the start that the murder would only be staged.
Babchenko left Russia in February 2017 after receiving threats.
He has contributed to a number of media outlets including top opposition newspaper Novaya Gazeta and is an avid blogger, accusing Russian authorities of killing Kremlin critics and unleashing wars in Ukraine, Syria and elsewhere.
Babchenko has recounted details of the operation to dupe the world into thinking he was dead, including donning a t-shirt with holes made to look like they were from gunshots and smearing himself with pig's blood.
Moscow has angrily denied any accusation of involvement in an assassination plot and says the staging was a "provocation" to discredit Russia.
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