U.S. forces at Soto Cano "were not involved in the flight that carried President Zelaya to Costa Rica on June 28," Southern Command spokesman Robert Appin said in an e-mail to The Associated Press. The American troops "had no knowledge or part in the decisions made for the plane to land, refuel and take off."
Appin said the U.S. troops at Soto Cano have stopped conducting exercises with the Honduran military since the coup.
"The U.S. military recognizes that the situation must be resolved by Hondurans and their democratic institutions in accordance with the rule of law," he said.
The administration of President Barack Obama has cut off millions of dollars in military and development aid to Honduras in an effort to pressure for Zelaya's reinstatement. It has stopped short of imposing trade sanctions that could cripple the Honduran economy, which is highly dependent on exports to the United States.
Zelaya, a wealthy rancher who aligned himself with leftist Venezuelan President Hugo Chavez during his presidency, has increasingly voiced frustration with Washington for failing to impose tougher penalties.
During a visit to Brazil last week, Zelaya spoke of the stop at Soto Cano, also known as Palmerola, and voiced suspicions of U.S. complicity in the coup - although he stressed that he did not believe the highest levels of the Obama administration were involved.
"The Obama administration has been firm in condemning the coup and demanding my restitution. I do not see reasons to believe that the Obama administration has two faces," Zelaya said.
"Now, there are some elements of the CIA that could have been involved. When they took me by plane to Costa Rica, it was a short flight but the plane made a stop at the Palmerola air base to refuel," he added. "Palmerola is a base administered by Honduran and U.S. troops. If it was a short flight, some 40 minutes, why did they have to refuel at Palmerola base?
Patricia Valle, who served as Zelaya's deputy foreign minister, reiterated those suspicions Saturday, although she gave no evidence that American personnel at the base interacted with the Honduran military officials on the plane or that they even knew Zelaya was there. She said Zelaya stayed on the plane during the stop.
"Zelaya was taken to Palmerola," Valle told the AP. "The United States was involved in the coup against Zelaya."
Palmerola was used by the United States during the Central American civil wars of the 1980s.
"Soto Cano Air Base belongs to the government of Honduras and is run and operated by the Honduran air force who make decisions about its use," Appin said.
The government of interim President Roberto Micheletti is trying to withstand international pressure to restore Zelaya before scheduled Nov. 29 presidential elections. It insists Zelaya was legally removed from office after violating court orders to call off a referendum asking voters whether they would support rewriting the constitution.
Micheletti voiced his own anger over Washington's stance on the coup, saying he hoped that U.S. Ambassador Hugo Llorens would not return to Honduras from a trip abroad. The U.S. Embassy has said Llorens left Honduras temporarily for personal reasons and has not been withdrawn from his post.
"I understand he is on vacation, so I hope he doesn't come back," Micheletti said Saturday during a meeting with more than 3,000 army reservists in the northern city of San Pedro Sula.
Associated Press writers Alexandra Olson in Mexico City, Alan Clendenning in Sao Paulo and Kathia Martinez in Tegucigalpa contributed to this report.