The witness, who was not named, worked at an airfield in the Ukrainian city of Dnipropetrovsk where he claimed to have seen a warplane take off on July 17 with air-to-air missiles and return without them.
An Investigative Committee statement said the testimony of the man "is important proof that Ukrainian military was implicated in the crash of the Boeing-777."
The MH17 flight from Amsterdam to Kuala Lumpur was shot down over territory in eastern Ukraine controlled by pro-Russian separatists, who have been fighting Kiev forces since April.
Ukraine and the West accuse Russia of supplying the rebels with a surface-to-air missile launcher, but Russia has issued several opposing theories, one of which involves a Ukrainian military jet allegedly seen next to the Boeing.
The statement by investigators comes the same day that Kiev and the separatists are to hold a new round of ceasefire talks, and shortly after Russian tabloid Komsomolskaya Pravda published an interview with the "secret witness" who said he worked at the airport on the day the Boeing 777 was downed.
The man, who was filmed by the paper with his back to the camera and even the back of his head blurred, said he saw a Sukhoi-25 jet take off armed with air-to-air rockets and return to the base without them.
"(The plane's operator) could have launched them into the Boeing out of fear or revenge," the witness said, identifying the pilot of the jet as Voloshin. "Maybe he mistook it for another plane."
Komsomolskaya Pravda claimed the witness showed up at its office by himself and that his identity checks out, but did not identify him because his family is still in Ukraine.
Investigative Committee said that the man, who is now officially a witness, may be enrolled in a witness protection program.
There was no evidence previously that Russian investigators had launched an official probe into the crash, in which citizens from 11 countries died, but no Russians.
Dutch authorities have been charged with establishing exactly what brought down the plane and are reconstructing part of the aircraft as part of their probe. Preliminary findings indicate only that the plane broke apart due to damage that came from outside.
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Strongman Putin is running out of his "magic touch" and it is getting increasingly difficult for him to take Russia to path of peace and prosperity. He is doomed and let's hope that Russia is not destined to go back to Yeltsin days with him.
The operative word is "secret witness". . When this tragedy first happened Russia tried to deflect their involvement by saying they had documented radar showing that the Ukrainian air force shot down this airliner -- of course they never provided evidence. They also ignored recorded conversations from the separatist to their Russian controllers discussing how they accidentally shot down the airliner and how to cover it up. Lastly - even the Ukrainian separatist admit they shot down the airliner - they just blame it on the Ukrainian govt for not declaring a no fly zone.