Morales spoke in Spanish to Aljazeera, which dubbed his comments into Arabic.
"The only terrorist in this world that I know of is Bush. His military intervention, such as the one in Iraq, that is state terrorism," Aljazeera quoted him as saying.
"There is a difference between people fighting for a cause and what terrorists do," Morales was quoted as saying.
"Today in Bolivia and Latin America, it's no longer people that are lifting their weapons against imperialism, but it's imperialism that is lifting its weapons against people through military intervention and military bases."
A Morales spokesman in La Paz, who was present during the interview, said he did not remember Morales saying that and that he must have been translated incorrectly.
Morales, who calls himself a nightmare for the United States, has alarmed the Bush administration with his opposition to its strategy in the war on drugs and his admiration for presidents Hugo Chavez of Venezuela and Fidel Castro of Cuba, both vocal foes of the United States.