Judge Miluska Cano agreed to hear charges from prosecutors, accusing Mr Humala of carrying out crimes as an army captain from 1991-1992.
The judge did not order Mr Humala to be held but ordered him to appear in court for the proceedings.
During his presidential campaign this year, Mr Humala insisted the charges were completely false and denied ever having violated human rights in his battle against guerrillas from the Shining Path and Tupac Amaru Revolutionary Movement.
Mr Humala's lawyer, Carlos Escobar, said the ruling was a "clear abuse of power" and charged that the judge's decision was politically motivated and instigated by the ruling APRA party.
Later at a news conference surrounded by legislators from his political party, Mr Humala said the charges were “political persecution," he said at a news conference surrounded by legislators from his political party.
"I've been a soldier who has defended the honour of my country and feel that now, for political purposes, not only do they want to destroy me, but this is the beginning (of an effort) to destroy the armed forces."
He described the charges as the "formal beginning" of the November 19 municipal and regional political campaign.
"I participated in the war, but I am not a human rights violator and I am going to ... defend my innocence, but I warn that this is part of a political campaign," he said.
Judge Cano denied any government or political pressure in her ruling.
In December, judge Cano dropped a case against then-candidate Garcia, who faced charges of covering up the massacre of more than 100 farmers by the military during his first term in office (1985-1990), saying there was not enough evidence to bring the case to trial.
If found guilty, Mr Humala faces up to 15 years of prison.
Mr Humala, 44, was defeated in a June 4 runoff vote by Alan Garcia, who received 52.5 percent of the vote against Humala's 47.5 percent.