Accused of atrocities committed by his regime from 1982 to 1990, Habre has lived in Senegal since 1990 until he was arrested this morning.
The former warlord turned head of state in the northern central African country appeared before the Court of Appeal in Dakar, which is set to rule on whether extradition to Belgium is possible.
He is currently in custody but Senegal’s Justice Minister Tidiane Sy won’t confirm where he is.
National radio has reported that the has been taken to a civilian prison in the capital, although this has not been confirmed by independent sources.
"We have shown the whole world that Hissene Habre was not above the law," said Ismael Hachim, president of the Association of Victims of Crime and Political Repression in Chad.
The former president, 63, is wanted in connection with activities by the Chadian intelligence services during his rule including "arbitrary and collective arrests, mass murders and systematic acts of torture, directed notably against members of certain ethnic groups in the country".
In 1992, two years after he was ousted in a coup by Chad's current President Idriss Deby and took up exile in Senegal, an official truth commission report accused Habre’s regime of some 40,000 political murders, of which 4,000 victims were officially named.