The deaths of protesters in the Ukrainian capital, Kiev, during anti-government demonstrations in February took place "under the direct leadership" of then-President Viktor Yanukovich, security chiefs have said.
The charges were made on Thursday by the prosecutor general and heads of the Interior Ministry and state security. They blamed the deaths of at least 100 demonstrators, many of whom were killed by police snipers, on the disbanded Berkut riot police.
Acting Interior Minister Arsen Avakov said Yanukovich issued the "criminal order" to fire at the pro-EU protesters, and agents from Russia's Federal Security Service (FSB) helped him plan and carry out the deadly assault between Feb. 18 and 20.
"FSB agents took part in both the planning and execution of the so-called antiterrorist operation," he said.
At least 12 members of the disbanded Berkut unit have been detained under suspicion of "mass murder."
Acting Prosecutor General Oleh Makhnitsky said that those detained included the head of a specialized company, which he called the "Black Unit," that operated within the Berkut riot police. The unit had allegedly handed out weapons for use against demonstrators.
"The police officers of this company were trained for special operations, including the killing of people. They were overseen by the presidential administration," Interfax Ukraine news agency quoted Makhnitsky as saying.
However, the identity of the snipers has been disputed.
Officials in Moscow believed far-right ultranationalists — rather than government forces — were responsible for carrying out the attacks on protesters, with the end goal of ousting Yanukovich.
In late February, the Interior Ministry disbanded the Berkut, whose name means "Golden Eagle" and signifies a predator capable of swooping quickly onto its prey.
Members of the Berkut police, former paratroopers and marines intended to fight organized crime in the country, knelt in front of a crowd in Lviv on Feb. 24 apologizing for their use of force during the anti-government protests.
In a separate development Thursday, Russia increased the gas price for Ukraine to $485 per 1,000 cubic meters and urged Kiev pay its $2.2 billion debt, in a move to further pressure an economy already on the brink of bankruptcy.
The head of Russia's top natural gas producer, Gazprom, told Russian Prime Minister Dmitry Medvedev that from this month the price would rise by 26 percent after Moscow introduced an export duty on gas to Ukraine.
"The gas price is increasing automatically from April," Alexei Miller told Medvedev, adding that the end of zero-export duties would trigger the rise.
The increase came just two days after Gazprom announced a 44 percent hike in the gas price for Ukraine starting April 1 to $385.50 per 1,000 cubic meters because of the unpaid bills.
The European Union receives around half of Russian gas via Ukraine.
Al Jazeera and wire services