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Mr Djibrine is accused of torturing and killing hundreds of opposition activists in the 1980s.
It is not clear whether he will be tried in Chad or in Senegal, where Mr Habre is due to go on trial after being held under house arrest there since 2005.
Mr Djibrine has not yet commented on the allegations.
He was arrested on the basis of a lawsuit filed 13 years ago by victims of Mr Habre's government.
Earlier this month, Senegal and Chad signed a deal to allow special judges to carry out investigations in Chad for Mr Habre's trial on charges of crimes against humanity. Under this deal, Mr Habre's former top officials can be tried alongside him in Senegal.
Mr Habre denies killing and torturing tens of thousands of his opponents.
Mr Djibrine is the former head of the Directorate of Documentation and Security (DDS), Mr Habre's political police force.
"He is accused of torture, acts of barbarism and illegal detention," prosecutor Massingaral Kagah told the AFP news agency.
He served in the United Nations peacekeeping force in Ivory Coast until campaigners complained and he was sent back to Chad.
The Chadian Association for the Defence of Human Rights said he should be put on trial in Chad.
For many years, Senegal resisted putting Mr Habre on trial but it has changed its position under new President Macky Sall.
The charges date from 1982, when Mr Habre came to power in a coup, until 1990, the year he was ousted.
A 1992 Truth Commission in Chad accused Mr Habre of being responsible for widespread torture and the deaths of 40,000 people.
He was accused of carrying out a deliberate policy of terror to discourage any opposition.
Survivors of torture say that, among other things, they were subjected to electric shocks, near-asphyxia and "supplice des baguettes", when their heads were squeezed between sticks.