MOSCOW — Five years after a missile shot down an airliner over a war zone in Ukraine, killing all 298 people on board, international prosecutors on Wednesday indicted three men with ties to Russian military and intelligence agencies, and implicated — but did not charge — a senior aide to President Vladimir V. Putin.

The criminal charges and the emergence of ever more detailed evidence against the Russian government, which has denied any role in downing Malaysia Airlines Flight 17, could further cool already icy relations between Moscow and the West.

[We look back at what happened to MH17 five years ago.]

At a news conference in the Netherlands, the Dutch-led investigative team announced charges against Igor Girkin, a former colonel in the F.S.B., the successor agency to the K.G.B.; and Sergey Dubinsky and Oleg Pulatov, both of whom have worked for the Russian military intelligence agency known as the G.R.U.

Prosecutors also charged Leonid Kharchenko, who is a Ukrainian citizen but led a Russian-backed separatist unit under the command of Mr. Dubinsky.