Judge Alejandro Solis ordered the arrest of Pinochet on Friday for 36 cases of kidnapping, one of homicide and 23 cases of torture at the Villa Grimaldi, a political detention centre run by Chilean secret police during his military regime .
"I am not going to give any details until Monday, when he will be legally notified," Solis said outside the court house.
Thousands of people were tortured at the Villa Grimaldi between 1974 and 1977.
Michelle Bachelet, the current Chilean president, and her mother were also held there for a time and mistreated.
Solis is in charge of the Villa Grimaldi investigation and questioned Pinochet this month about what happened at the former detention center in the Chilean capital of Santiago.
No birthday party
Pinochet was forced to cancel celebrations for his 90th birthday last November after he was placed under house arrest on charges related to the disappearance and presumed death of three left-wing opponents during his rule between 1973 and 1990.
Bachelet and her mother were
held at Villa Grimaldi
The house arrest, also on charges of tax fraud, lasted for seven weeks, ending in early January when he was granted bail.
Pinochet has been diagnosed with mild dementia caused by frequent mini-strokes and he has avoided trial in other human rights cases on the basis he was too ill to stand trial.
"I don't think it has been proven that he is mentally ill," said Solis, who last met the former dictator on October 18 and remarked on how healthy Pinochet was looking.
During that meeting with the judge, Pinochet denied responsibility for the torture of opponents at Villa Grimaldi.
Pinochet was first arrested in 1998 in London on an international warrant issued by Baltazar Garzon, a Spanish judge.
He was released in 2000, after 16 months of house arrest, on the grounds he was medically unfit to be tried.