Austria's decision to search the plane of President Evo Morales was an act of aggression and a violation of international law, Bolivia said.
Mr Morales' plane was diverted after France and Portugal abruptly cancelled air permits for Mr Morales' plane en route from Moscow.
The cancellation is thought to have been due to fears fugitive ex-US spy agency contractor Edward Snowden could be on board.
Bolivian and Austrian officials denied this.
Austrian authorities inspected Mr Morales' government plane at Vienna airport this morning and found no unauthorised people on board, Deputy Chancellor Michael Spindelegger said.
"Our colleagues from the airport had a look and can give assurances that no one is on board who is not a Bolivian citizen," Mr Spindelegger told reporters at the airport.
He said rumours that Mr Snowden might be on board were untrue.
Bolivia's Ambassador to the United Nations Sacha Llorentty Solz told reporters in Geneva that he had no doubt that the orders to divert Mr Morales's plane came from the United States.
Mr Morales' plane has now left Vienna.
Earlier, Interior Minister Johanna Mikl-Leitner said Austria allowed the plane to land because it did not share other countries' worries that Mr Snowden might be on board.
"Austria did not close its airspace and the plane could of course land although many other countries apparently feared that Snowden was on board too," the minister told ORF radio.
"Austria did not do that, which means there is no fear here."
Wanted by the US for espionage after divulging classified details of US phone and internet surveillance, Mr Snowden apparently remains in the transit area of Moscow's Sheremetyevo airport.
He applied for asylum in Austria - and several other countries, including Ireland - via the country's Moscow embassy on Monday, which the government said was insufficient to grant him refuge.
Ms Mikl-Leitner said it would be up to Austrian asylum authorities to decide what to do in the unlikely case that Mr Snowden arrived there.
She defended Austria's position that Mr Snowden would have to apply in person for asylum, saying this was clearly spelled out in the law.
"This is in the hands of the authorities and independent courts. The important thing here is that this would be judged individually, as in every other case," she said.