Colombia has acknowledged that its aircraft may have "accidentally" entered Ecuador's airspace last week in an operation against left-wing rebels.
The Ecuadorean president visited the border zone on Thursday
The defence ministry apologised for any unintentional incursion and said it would not happen again.
Ecuador earlier said it was considering recalling its ambassador to Colombia over the border incursion.
Colombian rebels often cross into Ecuador and the issue of patrolling has been a cause of friction in the past.
On Thursday, Ecuadorean President Alfredo Palacio inspected the area where the incident was said to have taken place.
His visit came after it was announced that Ecuador had destroyed a camp allegedly used by Colombia's largest rebel group, the Farc, in its territory.
Colombian Black Hawk helicopters and warplanes allegedly strayed into Ecuadorean territory on Saturday, in an operation against leftist guerrillas.
Local media had accounts from witnesses and police of ground battles taking place and recovered spent ammunition.
Quito issued a formal protest and demanded an apology for the "violation of their sovereignty".
It is not the first time that Ecuador has denounced an alleged incursion by Colombian planes along the 580-km (360-mile) border the two countries share - similar complaints were made last year.
The country has remained neutral in Colombia's struggle against a 41-year-old Marxist insurgency, despite requests for assistance.