Ecuador says it is "deeply concerned" by confirmation that an Ecuadorean was among those killed when the Colombian military launched a cross-border raid.
The dead man's family insist he had no links with Colombian rebels
The Ecuadorean government said it would appeal to the Organisation of American States (OAS) for help in the matter.
Colombia on Sunday confirmed that an Ecuadorean died when its troops attacked a rebel camp three weeks ago.
The raid provoked the worst regional tensions in recent years, with Ecuador breaking off diplomatic relations.
Colombian forces attacked the Revolutionary Armed Forced of Colombia (Farc) camp located just across the border in Ecuador on 1 March.
A senior Farc commander, Raul Reyes, and more than 20 other people, including four Mexican nationals, were killed.
Aerial photos show the ruins of the Farc camp inside Ecuador
Colombian Defence Minister Juan Manuel Santos confirmed that an Ecuadorean national was among the dead and that his body had been taken to Colombia.
His Ecuadorean counterpart, Wellington Sandoval, said that the news "complicated" bilateral relations.
"Things have become complicated, because an Ecuadorean has died in an attack by a foreign country," Mr Sandoval said.
Ecuador's President Rafael Correa had earlier warned of grave diplomatic consequences if it were proved that an Ecuadorean had died in the raid.
The Ecuadorean authorities say fingerprint records show the dead man is Franklin Aisalia Molina, while Mr Aisalia's family said they identified his body from news photos.
In a statement, the Ecuadorean foreign ministry said the killing of Mr Aisalia and the transfer of his body to Colombia was a human rights abuse and a violation of international law.
"Ecuador will appeal to the Secretary General of the OAS with the aim of finding a definitive solution to this case," the statement said.
Any "positive explanations" that Colombia could give Mr Aisalia's family "will create an atmosphere conducive to establishing a climate of confidence between the two nations."
Colombia's defence ministry had earlier said the dead man appeared to have been a member of the Farc who specialised in helping rebels cross into Ecuador to hide.
Mr Aisalia's family has denied this.
Ecuador and Venezuela sent troops to their borders after Colombia's raid, withdrawing them several days later after a meeting of regional leaders in the Dominican Republic.
But tensions remain.
On Monday, Venezuelan President Hugo Chavez said comments by the Colombian officials defending the raid could risk a new diplomatic crisis.
"For the love of God," Mr Chavez said in remarks directed at his Colombian counterpart, Alvaro Uribe, "take good care with spokesman of war like your defence minister."
Mr Santos had said the rebel camp had been a legitimate military target.