Bolivia accused the United States of ordering European countries to block President Evo Morales's flight from their airspace, and accused European governments of "aggression" by thwarting the flight.
However, it is still unclear whether European countries did block the plane and, if so, why. French, Spanish and Portuguese officials all said today the plane was allowed to cross their territory.
Snowden himself remains out of public view, believed to be stuck in a Moscow airport transit area, seeking asylum from one of more than a dozen countries.
The plane carrying Morales home from a Moscow summit was rerouted to Vienna late yesterday, adding a new twist to the international uproar over Snowden's revelations of widespread US surveillance. The plane took off again shortly before noon today after sitting overnight at the airport.
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The emergency stop in Austria may have been caused by a dispute over where the plane could refuel and whether European authorities could inspect it for signs of Snowden.
Bolivian and Austrian officials both say Snowden was not on board.
Bolivian officials said that France, Portugal and Italy blocked the plane from flying over their territories based on unfounded rumours that Snowden was on board. The ambassador to the United Nations, speaking in Geneva today, continued to insist that several European countries had refused permission for the plane to fly in their airspace.
Sacha Llorenti said it was an "act of aggression" and that the four countries violated international law. Llorenti said "the orders came from the US" but other nations violated the immunity of the president and his plane.