"It is obvious that different versions are being considered, including the version - you know what we are talking about - let's say, a deliberate atrocity," Kremlin spokesman Dmitry Peskov told reporters when asked about the investigation.
Asked if the International Civil Aviation Organisation would investigate the crash, Peskov said that the circumstances made it different, although he cautioned that investigators had made no formal conclusions yet about what exactly took place.
"Let's wait for the results of our Russian investigation," Peskov said.
The private Embraer jet on which Prigozhin was travelling to St Petersburg from Moscow crashed north of the capital killing all 10 people on board on August 23, including two other top Wagner figures, Prigozhin's four bodyguards and a crew of three.
The cause is still unclear but villagers near the scene told Reuters they heard a bang and then saw the jet plummet to the ground.
The plane crashed exactly two months since Prigozhin took control of the southern city of Rostov in late June, the opening salvo of a mutiny which shook the foundations of President Vladimir Putin's government.
Russia has informed Brazil's aircraft investigation authority that it will not probe the crash of the Brazilian-made Embraer jet under international rules "at the moment," the Brazilian agency told Reuters.
Asked about that report, Peskov said: "First of all, the investigation is under way, the Investigative Committee is engaged in this."
"In this case there can be no talk of any international aspect," Peskov said.
In an unusual move, the Interstate Aviation Committee (IAC), which oversees aviation accident investigations in a grouping of former Soviet republics including Russia, said it was not investigating the crash, adding that it would not be commenting on the "circumstances of the incident".
The day after the crash, Putin sent his condolences to the families of those killed and said he had known Prigozhin for a very long time, since the chaotic years of the early 1990s.
"He was a man with a difficult fate, and he made serious mistakes in life," Putin said, while describing him as a talented businessman.
The Kremlin has rejected as an "absolute lie" the suggestion by some foreign politicians and commentators - for which they have not provided evidence - that Putin ordered Prigozhin to be killed in revenge.
US President Joe Biden has said he was not surprised by the death and that not much happened in Russia that Putin was not behind.
After Prigozhin's death, Putin ordered Wagner fighters to sign an oath of allegiance to the Russian state - a step that Prigozhin had opposed due to his anger at the defence ministry that he said risked losing the Ukraine war.
Followers of Prigozhin laid flowers, messages and poetry at his grave on Wednesday, hailing him as a fearless warrior.
