Ollanta Humala, a former army officer, is facing charges that troops under his command committed murder and torture when he was the commander of counter-insurgency forces in the 1990s.
On Thursday, judge Miluska Cano ordered Humala to remain in the country and set bail at $6,000, ruling there was sufficient evidence to open a criminal case.
Humala, defeated by Alan Garcia in a June runoff for the presidency, has denied any wrongdoing.
Carlos Escobar, his lawyer, told the radio station CPN: "There is no proof of murder or of injuries."
The charges are based on testimony from witnesses who say that a married couple - Natividad Avila and Benigno Sullca - were dragged from their home by soldiers under Humala's command in 1992 in the village of Pucayacu.
Avila's sister, Teresa, said in a sworn statement that she found her brother-in-law shot dead and that her sister's body was never found.
Local media reported recently that her brother, Jorge, retracted allegations that he was tortured for eight days on the Madre Mia jungle military base in the presence of Humala, its commander. He reportedly said he was pressured into making the claim by overzealous human rights groups.
But human rights officials called for an investigation after other news reports suggested Avila had been paid off to deny his charge against Humala.
Humala, who retired from the army as a lieutenant-colonel, acknowledges commanding the Madre Mia counter-insurgency base and using the pseudonym Captain Carlos during the fight against fighters from the Maoist group the Shining Path.
Escobar said Humala is the victim of political persecution because he is the "principal representative of the opposition" against Garcia's government.