Habre, dubbed "Africa's Pinochet," was sentenced by a special African court to life in jail in 2017 for crimes against humanity.
More than 40,000 people are thought to have been murdered during his rule.
"There are around 10,800 victims, who each have received 925,000 CFA francs ($1,529)," president of Chad's human rights commission, Djidda Oumar, told AFP.
"We divided the money equally, with direct and indirect victims (families of those killed) receiving the same amount."
The payments, which began February 23, amount to less than 10 percent of the total sum awarded to victims by courts in Senegal and Chad, according to the International Commission of Jurists (ICJ).
Habre ruled Chad from 1982 until he was ousted by Idriss Deby Itno in 1990 and fled to Senegal.
In April 2017, Dakar's appellate court mandated the African Union to find 82 billion CFA francs for victims by searching Habre's assets and soliciting contributions, the ICJ added.
But the fund is not yet operational and many victims have died without receiving any compensation.
In a separate trial in 2015, a Chadian court convicted about 20 Habre-era security agents to pay half of 75 billion CFA francs awarded to victims, with the government paying the other half.
The former dictator served his sentence in Senegal where he died aged 79 from Covid in August 2021.
Victims of Former Chad Dictator Habre Receive Government Compensation
FILE—In this November 25, 2005 photo, former Chad dictator Hissene Habre leaves a court in Dakar, Senegal. Habre's government was accused of killing tens of thousands. He became the first former head of state to be convicted of crimes against humanity by an African court.
LIBREVILLE, Gabon — More than 10,000 victims of Chad's former dictator and convicted war criminal Hissene Habre have begun to be paid government compensation totaling $16.5 million, NGOs announced on Tuesday.