Gustavo Larrea, Ecuador's interior minister, said the human rights of "hundreds of citizens were systematically violated" during parts of the 1980s and 1990s when the government fought to put down a series of relatively minor leftist uprisings.
He said there have been 327 cases of political assassinations, torture and disappearances that have gone unpunished during the period.
"Impunity has made society, the state, close their eyes to the events that occurred in the country in a planned and systematic manner," he said.
Members of the victims' families and human rights groups accuse the 76-year-old Febres Cordero, for decades a dominant figure in Ecuadorean politics, of ordering political killings during his government. He has strongly denied the accusations.
Ex-president hits back
Febres Cordero, speaking at a press conference in his native port city of Guayaquil, accused Correa on Friday of forming "a tribunal of the Inquisition" and said his political enemies want to try him "for having fought terrorism".
He also called Correa "a totalitarian" and said that if the government sought to proscute him, he would not flee.
"I've never run, nor will I run," he said. "If they want to look for me, they know where to find me."
The commission will have nine months to present a report, with a possible extension of three months.