The 33-year-old helicopter navigator is charged with acting as an accessory in the murder of two Russian journalists "with motives of political hatred."
She is also charged with illegally crossing the border into Russia prior to her detention in a Moscow jail nine months ago.
Russia portrays the case as a legal matter involving freedom of the press covering the war between Ukraine's government and pro-Russian insurgents in eastern Ukraine.
Considered a symbol of resistance against what most Ukrainians call a Russian-created insurgency, she was even elected to parliament in absentia.
Savchenko has also garnered international attention with a hunger strike in her Moscow prison that she broke off in March, after more than 80 days, because of severe health problems.
Ukraine's President Petro Poroshenko and the European Union have urged Russia to release her, as have rights groups including Amnesty International.
According to Russian officials, Savchenko handed information to Ukrainian forces on the movements of two Russian television journalists killed in a mortar attack in eastern Ukraine in June last year.
"An artillery strike was then directed exactly at these coordinates, as a result of which VGTRK journalists Igor Kornelyuk and Anton Voloshin died," it said.
The journalists were killed close to a rebel checkpoint on June 17 2014. Kiev has denied they were targeted.
The Investigative Committee said it had "incontrovertible proof" of her guilt including analysis of shrapnel and satellite images, as well as Savchenko's written admission "confirming her involvement in directing fire."
"We will appeal the charges," he said.
In addition to the murder charges, Russia accuses of Savchenko of illegally entering from Ukraine "pretending to be a refugee".
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