Habre served as dictator from 1982 until 1990, when he was deposed by President Idriss Deby Itno and fled to Senegal, where he has been living since.
The Extraordinary African Chambers were established in the Senegalese court system in February to prosecute Habre's alleged crimes.
The chambers' chief prosecutor, Mbacke Fall, asked to have Habre taken into police custody, Human Rights Watch said, and he was arrested Sunday.
The prosecutor is expected to charge Habre before his period of detention expires.
If Habre is charged, the pretrial investigation is expected to last 15 months, and a trial could begin in 2014 or 2015.
"I have been waiting more than two decades to see Hissene Habre in court," said Clement Abaifouta, who was a political prisoner during Habré's rule, told Human Rights Watch. "We are finally going to be able to confront our tormentor and regain our dignity as human beings."
Habre was previously charged in Senegal in 2000, but the country's courts said he could not be tried there at the time.