Ecuador says it is investigating what it describes as a violation of its airspace by the Colombian military.
Defence Minister Oswaldo Jarrin said a Colombian aircraft had been picked up by Ecuadorean radar at the weekend.
Colombia denied over flying Ecuadorean territory, but said the aircraft had been deployed after an attack by rebels, who then escaped into Ecuador.
It is the latest of a series of incidents along the border that have provoked diplomatic tension.
Colombia has been fighting an offensive by the country's largest guerrilla group, the Farc, in the region.
Last month, the government of Bogota issued an apology after one of its aircraft "accidentally" entered Ecuador's airspace in an operation against Farc rebels.
Ecuador responded by stepping up radar surveillance along the 580km (360m) border the two countries share.
Colombian and Ecuadorean officials will discuss the issue at a meeting of military officials on Tuesday.
Ecuador has remained neutral in Colombia's struggle against a 41-year-old Marxist insurgency, despite requests for assistance.