The men are set to be prosecuted in a trial scheduled to start on March 9, 2020.
"We now have the information and proof that the Russian Federation is involved in this tragedy, in this crime," Dutch chief prosecutor and JIT coordinator Fred Westerbeke said at a MH17 press conference in Nieuwegein, Netherlands.
The JIT worked alongside the Australian Federal Police last year when they confirmed flight MH17 was gunned down by a Russian army BUK -M1 missile. It was brought to a field in Pervomaisky, eastern Ukraine from a military base southwestern Russia.
All suspects have military backgrounds, whereas Mr. Kharchenko of Ukraine was the leader of a separatist group at the time of the incident.
Australia's Foreign Minister Marise Payne issued a statement on the charges, saying: "The downing of MH17 was a despicable act and the Australian Government has not stopped in the pursuit of justice for the 298 victims, including 38 Australians."