"It is not an arrest for expulsion," said lawyer Doudou Ndoye on Saturday, who accused the government of violating Habre's human rights.
He said Habre, who is wanted in Belgium on charges relating to atrocities committed during his 1982-1990 rule, had been taken to the police criminal investigation division.
The reasons for his latest detention were not immediately clear.
On Friday, he had been released after 10 days in custody when a Senegal court disqualified itself from ruling on the extradition request from Belgium.
The prosecution chamber of the Dakar Court of Appeals declared itself "not competent" to rule whether to issue an extradition order for 63-year-old Habre, who has lived in exile in Senegal for 15 years.
The former president known as "Africa's Pinochet" is wanted by Belgium to face trial for alleged mass murder and torture under a law that allows Belgian courts to try cases of human rights abuses in other countries.
A truth commission report in 1992 said his regime was responsible for about 40,000 political murders, of whom 4000 victims have been officially named.
The charges he is being asked to face in Belgium were filed in 2000 by Belgians of Chadian origin who were victims of atrocities committed by Habre's intelligence services.
Belgium has said that if the extradition attempt fails, it has other tools to bring Habre to justice such as the UN convention on torture.