Bolivia filed a complaint at the United Nations on Wednesday over what it called the kidnapping of its president, Evo Morales, whose plane was diverted to Vienna amid suspicions that it was carrying the surveillance whistleblower Edward Snowden.

The country's ambassador to the UN, Sacha Llorenti, said the enforced rerouting to Austria was an act of aggression and a violation of international law. The US admitted that it had been in contact with other nations over potential flights by Snowden.

"We will demand appropriate explanations from those countries that submitted to North American imperialism and briefly put President Morales in such a helpless situation," Llorenti told the state radio Patria Nueva. Bolivia's vice-president, Alvaro García Linera, said Morales was "kidnapped by imperialism".

South American nations accused the United States of being behind the extraordinary manoeuvring, furious at what they regarded as the humiliation of Morales. In Washington, the state department would not comment on the Morales flight but conceded that it discussed the issue of flights by Snowden with other nations.

"We have been in contact with a range of countries that had a chance of having Snowden land or travel through their country but I am not going to outline what those countries were or when this [contact] happened," said spokeswoman Jan Psaki.

The diplomatic crisis may have been set off by a remark by Morales during a television interview in Russia, where he had been attending an energy conference. Morales said that he sympathised with Snowden, who is believed to be holed up in the transit area of Sheremetyevo airport, and hinted that Bolivia might accept an asylum petition. "If there were a request, of course we would be willing to debate and consider the idea," Morales told RT Actualidad, the Spanish-language service of the Russian broadcaster RT.

Later that day, soon after Morales was bound for La Paz, Spain, Italy, France and Portugal refused to allow the presidential jet to fly through their airspace over suspicions that Snowden was on board, according to the Bolivian government's account.

The Bolivian foreign minister, David Choquehuanca, said France and Portugal were the first to cancel air permits. "They say it was due to technical issues, but after getting explanations from some authorities we found that there appeared to be some unfounded suspicions that Mr Snowden was on the plane. We don't know who invented this lie. We want to denounce to the international community this injustice with the plane of Evo Morales," Choquehuanca said.

Diverted from their planned route, pilots feared they would not be able to complete their journey. The plane was eventually cleared to land in Vienna, where Morales was forced to spend 13 hours in humiliating limbo while officials worked to resolve the dispute.

It later took off after Austrian officials said Snowden was not on board. But it was unclear whether any officials in Vienna had searched the plane. Austria's deputy chancellor, Michael Spindelegger, said Morales "agreed to a voluntary inspection". But the Bolivian defence minister, Ruben Saavedra, later said Morales had refused entry to the inspectors, and that they had only got as far as the door of the aircraft.

In Bolivia, the treatment of the president stirred up patriotic and anti-imperialist sentiment. Several labour and indigenous organisations planned a welcome rally for the president on his arrival in La Paz on Wednesday evening.

The Argentinian president, Cristina Fernández de Kirchner, attacked the "vestiges of colonialism" in a speech in Buenos Aires. "We believe this constitutes not only the humiliation of a sister nation but of all South America," she said. An emergency meeting of the Union of South American Nations was expected to be convened on Thursday.

It was widely assumed in South America that Washington was responsible for the presidential plane being refused air permissions. Earlier in the week, the state department said it hoped Snowden would be returned to the US to face charges of espionage and theft after a string of other countries said they would not accept his applications for asylum.

Speaking before the developments in Vienna, the state department rejected claims made by Snowden on Monday that the US had bullied other potential hosts, such as Ecuador, into withdrawing their offer of asylum. The US says it has only impressed upon possible host countries the seriousness of the crimes with which Snowden had been charged.