The crisis in Honduras, where members of the country’s military abruptly awakened President Manuel Zelaya on Sunday and forced him out of the country in his bedclothes, is pitting Mr. Obama against the ghosts of past American foreign policy in Latin America.

The United States has a history of backing rival political factions and instigating coups in the region, and administration officials have found themselves on the defensive in recent days, dismissing repeated allegations by President Hugo Chávez of Venezuela that the C.I.A. may have had a hand in the president’s removal.

Obama administration officials said that they were surprised by the coup on Sunday. But they also said that they had been working for several weeks to try to head off a political crisis in Honduras as the confrontation between Mr. Zelaya and the military over his efforts to lift presidential term limits escalated.