Colombia, a staunch US ally, says it never violated Ecuador's sovereignty in the operation that killed 17 rebels, including Raúl Reyes, the most senior rebel ever to be killed in combat in the more than 40 years since the rebels rose up against Colombia's government.
But Ecuadorean President Rafael Correa recalled his ambassador to Colombia and said that Ecuador "will not allow any more offenses by the Colombian government."
He also warned such actions might result in the "ultimate consequences."
Venezuelan President Hugo Chávez, who considers Mr. Correa an ally in his efforts to unite Latin American nations against the US, issued a public warning to Colombia's conservative president, Álvaro Uribe.
"You had better not get the idea of doing this on our territory because it would be a cause for a war," said Mr. Chávez.
Relations between Mr. Uribe and Chávez soured last fall over the Venezuelan leader's efforts to secure the release of rebel-held hostages.
The strike will make reconciliation harder, say analysts.
Colombia has not responded to Chávez's comments but said it would reply to Ecuador's formal protest, defending the action of its military.
"Colombia did not violate sovereignty but acted according to the principle of legitimate defense," the Colombian Foreign Ministry said in a statement Sunday.
Under Uribe's security policies, rebels have been driven to remote, rural areas of Colombia and have seen their ranks slashed by desertions, casualties, and captures.
Mr. Reyes's death is a "devastating blow" to the Revolutionary Armed Forces of Colombia (FARC), says Alfredo Rangel of the Bogotá-based Security and Democracy Foundation, adding that the rebels would now have to "reconsider whether their armed struggle is still valid."
Reyes was widely considered to have been next in line to succeed legendary FARC founder Manuel "Sureshot" Marulanda.
Reyes was the FARC's spokesman and one of the top negotiators during failed peace talks with the government of Andés Pastrana from 1998 to 2002, during which he led a FARC commission on a tour of several European nations.
Reyes was wanted in connection with 57 murders and four cases of kidnapping, according to the general prosecutor's office. He also faced charges for 26 counts of terrorism and 25 for rebellion.
Colombia's Defense Minister Juan Manuel Santos said that, in Saturday's operation, ground troops in pursuit of the rebels were fired on from within Ecuadorian territory and aircraft were called in to bomb the location from Colombian airspace.
Colombian police were then sent into Ecuador to secure the base and retrieve the bodies of Reyes and a second rebel commander killed in the raid.
Correa said his own troops sent to the area had found the bodies of 15 rebels in a makeshift camp in their underwear.
"There was no pursuit," he said angrily. "They were bombed and massacred while they slept."
• Material from the Associated Press was used in this report.