The situation drew a swift rebuke from Ecuador's foreign minister, who told reporters he planned to call a regional meeting of the Union of South American Nations, known as UNASUR, to discuss it.
"We consider this a huge offense, and I will call for a UNASUR special summit with foreign secretaries to discuss this issue," Ecuadorian Foreign Minister Ricardo Patino said.
Cuba's Foreign Ministry released a statement condemning the incident.
"This constitutes an unacceptable, unfounded and arbitrary act which offends all of Latin America and the Caribbean," the statement said.
A history of tense relations
It isn't the first time Bolivian authorities have accused U.S. officials of trying to meddle with their presidential plane.
In 2011, Morales said he was worried that U.S. authorities would plant something on his presidential plane to link him with drug trafficking when he attended a United Nations General Assembly meeting.
"I think they have to be preparing something," he told a convention of female farm workers. "So much that I'm afraid to go with our airplane to the United States."
Bolivia and the United States have had diminished relations since September 2008, when each country expelled the other's ambassador.
Morales, a strong proponent of the cultivation of coca plants -- the source of cocaine -- expelled the U.S. Drug Enforcement Administration a month later. He also delivered a strong verbal criticism of the U.S. government at the United Nations General Assembly that year.
In May, Morales said he was expelling the U.S. Agency for International Development from his country for allegedly meddling and conspiring against the government.
The U.S. State Department denied the accusation, called the decision regrettable and said the ones who will be hurt by the expulsion will be ordinary Bolivians.