The L-410 plane carrying 22 people crashed around 9:23am local time (0623 GMT) during a flight over the republic of Tatarstan, the ministry said on its Telegram channel.
"Six people were rescued, 16 were taken out without signs of life," the ministry said.
The ministry had earlier said that 15 people died and that the aircraft was carrying 23 people.
Images published by the ministry showed the aircraft broken in half with a severely dented nose. The six survivors were being hospitalised, the local health ministry told the Interfax news agency.
Tatarstan head Rustam Minnikhanov was travelling to the scene of the crash, a statement on his website said.
According to Interfax, the plane belonged to the Voluntary Society for Assistance to the Army, Aviation and Navy of Russia, which describes itself as a sports and defence organisation.
The head of the organisation's regional branch said the parachuting club that organised the flight was not to blame.
"We are the best, we are among the top five clubs," Ravil Nurmekhametov told TASS news agency, adding that the club had hosted European and World championships.
The Czech-built L-410 light aircraft was one of the two planes used by the club, according to its website. Two L-410 planes suffered fatal accidents in Russia earlier this year, leaving a total of eight people dead.
Russia was notorious for plane accidents but has improved air traffic safety in recent years with major airlines switching from Soviet aircraft to modern jets.
But poor aircraft maintenance and lax safety standards still lead to frequent accidents in far-flung regions involving light aircraft, with occasional large-scale tragedies.
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