The German Grand Prix had been scheduled for June 21, followed by the Dutch TT at Assen on June 28 with Finland's new KymiRing making its debut on July 12.
The Dutch race was the only venue to have featured on the world championship calendar in every year since it started in 1949.
"It is with great sadness that we announce the cancellation of these three important Grands Prix on the MotoGP calendar," said Carmelo Ezpeleta, chief executive of promoters Dorna, in a statement.
Ezpeleta had said last week that he was optimistic of racing from July.
MotoGP's season has yet to start, with the first 11 races affected by the virus, and organisers have yet to publish a fully revised calendar.
Races in Spain, France and Italy have been postponed and are looking uncertain.
The next race on the original calendar is the Czech Grand Prix in Brno on August 9.