Foreign Minister Jose Manuel Garcia Margallo said Spain had nothing to apologise for, however, denying allegations that Madrid had refused overfly rights for the Bolivian leader’s plane.
Margallo did not identify who provided the apparently faulty intelligence that Snowden was aboard the presidential jet.
“I work with the information they give me. They told us that it was clear that he was inside,” the foreign minister said in an interview with Spanish public television.
“I cannot verify if it is true or not true at the moment they tell me — you have to act immediately.”
Bolivia reacted furiously after Morales, flying home from Moscow on Tuesday, had to land in Vienna, accusing several European nations of denying his jet overfly rights.
The plane resumed its journey on Wednesday and refuelled in Las Palmas on the Spanish archipelago of the Canary Islands.
Margallo denied Spain had closed its airspace to the Bolivian leader’s plane, saying that despite the intelligence he had trusted Bolivia’s written guarantee that Snowden was not aboard.
“I believe in the word of friendly countries and Bolivia is one,” the foreign minister said.
“What Spain said was that in no case was it going to restrict its airspace and that it would keep its authorisation in force so the plane could land and refuel in Las Palmas,” Margallo said.
“There is no need for any apology to Bolivia.”
Bolivia accused France, Portugal, Italy and Spain of denying flyover rights because of Snowden, who is seeking to avoid US espionage charges after leaking embarrassing details of a vast US phone and Internet surveillance programme.
The 30-year-old is believed to be holed up at a Moscow airport looking for a country that will give him safe haven.
“I found the treatment of the president of Bolivia ridiculous and completely unacceptable,” the president of the European parliament, German politician Martin Schulz, said during a visit to Madrid.
“I think we should check who gave the orders for this,” he told an economic forum.
Bolivia is one of 21 countries to which Snowden has asked for asylum. Morales said earlier this week that his country would be willing to study the request.
The Bolivian president has threatened to close the US embassy in Bolivia over the jet diversion, which he said was the result of Washington putting pressure on European nations.
Bolivia’s Latin American allies have also responded with outrage to the incident.
Venezuelan President Nicolas Maduro said Thursday his country was reviewing its relations with Madrid, describing the actions of the Spanish government “vile”.
But Spain’s foreign minister said the reaction was sparked by a “lack of knowledge of the facts in the heat of all these stories”.
Margallo said he had asked Spain’s ambassador in Caracas to explain what happened to the Venezuelan authorities.