Spain and other European countries were told that US whistleblower Edward Snowden was on board the Bolivian president's plane earlier this week, the Spanish foreign minister has said.
Jose Manuel Garcia-Margallo refused to say who gave out the information.
The plane carrying Bolivian President Evo Morales from Moscow back to La Paz was grounded for 13 hours in Austria earlier this week after it was banned from European airspace.
Edward Snowden was not found on board.
The incident has been widely condemned by President Morales and several other South American nations, who have demanded an apology from the countries involved.
"They told us they were sure... that he was on board," Mr Garcia-Margallo told Spanish television, without indicating who "they" are.
"And so the reaction of all the European countries that took measures - whether right or wrong - was because of the information that had been passed on. I couldn't check if it was true or not at that moment because it was necessary to act straight away."
Mr Garcia-Margallo denied reports that Spain - along with France, Portugal and Italy - had closed its airspace to the plane.
He said the delay in Austria meant the flight permit had expired and had to be renewed, so there was "no need to apologise".
Mr Garcia-Margallo's comment is the first official recognition by the European states that the incident with Mr Morales' plane was connected with the Snowden affair.
Spain will be keen to limit the diplomatic damage as it does a lot of trade with countries in Latin America, the BBC's Tom Burridge reports from Madrid.
France earlier apologised for the plane incident, blaming it on "conflicting information".
Embassy closure threat
President Morales' plane was rerouted on Tuesday as he travelled from a meeting in Russia where he had suggested he would be willing to consider an asylum application from Mr Snowden.
The former CIA contractor is believed to be holed up at the transit area of Moscow airport after leaking details of a vast US surveillance programme.
He has sent requests for political asylum to a number of countries, including Bolivia.
Mr Morales was joined by the presidents of Argentina, Uruguay, Ecuador, Venezuela and Suriname at a meeting on Thursday to discuss the incident.
The leaders demanded an explanation from France, Portugal, Italy and Spain over their actions and, although the US was not mentioned in their statement, several of them criticised the Americans in comments after the meeting.
The Bolivian president blamed Washington for pressurising European countries into refusing him passage, and threatened to close the US embassy in La Paz.
"We have dignity, sovereignty. Without America, we are better off politically and democratically," he said.
The US state department has not commented directly on the latest claims, saying only that Washington had "been in touch with a broad range of countries" over the Snowden case.
Demonstrators marched on the French embassy in La Paz on Wednesday, burning the French flag and demanding the expulsion of the ambassador to Bolivia.
Mr Morales' plane took off from Vienna on Wednesday morning and arrived back in La Paz on Wednesday night.