Judge Jazmin Barrios pressed ahead Friday despite another judge's ruling Thursday that the charges should be nullified due to a legal technicality, the Los Angeles Times reported.
Rios Montt appeared in court Friday but his defense team did not, leading Barrios to postpone the trial's start, the newspaper said.
Hundreds of protesters outside the courthouse in the capital Guatemala City chanted slogans and held placards.
Rios Montt, 86, is accused of ordering the military to kill the Ixil Maya in 1982 and 1983 -- including women, children and the elderly -- as part of the nation's bloody 36-year civil war.
Descendants of the ethnic group held signs in Spanish reading, "We youth have a right to know the truth."
Prosecutors have three days to address the annulment, otherwise they will have to start over with new charges.