Mr Sandoval stoked controversy after Colombia's raid on a Farc camp
The defence minister of Ecuador has resigned unexpectedly amid a row with neighbouring Colombia over a cross-border raid on a rebel camp.
The resignation of Wellington Sandoval was confirmed by Deputy Defence Minister Miguel Carvajal.
His replacement, Javier Ponce, is expected to be sworn in later on Wednesday, reports said.
Mr Sandoval had stoked controversy with comments he made after a Colombian raid on a Farc camp inside Ecuador in March.
Farc guerrilla leader Raul Reyes was among 25 people killed in the attack, which sparked fears of a regional war.
Mr Sandoval had been highly critical of the Colombian government in the aftermath of the attack.
He was also quoted as saying in an interview with the Quito daily El Comercio that he was aware Reyes often entered Ecuador to escape Colombian troops.
"We knew that Reyes crossed into Ecuador frequently," Mr Sandoval was quoted as saying.
His resignation comes just days after he strongly rejected the possibility that he might leave the government of President Rafael Correa.
Mr Correa made highly critical comments about Ecuador's intelligence services last week, saying they were being manipulated by the CIA, the US foreign intelligence agency.
Mr Ponce, who is currently serving as Mr Correa's personal secretary, has a background in journalism.