The July verdict followed the May sentencing of Habre to life for war crimes and crimes against humanity
A special African Union court ruled in July that Habre should give up to 30,000 euros ($33,000) to each victim of abuses committed during his 1982-1990 rule, as well as to their relatives.
Philippe Houssine, a lawyer for victims under Habre's rule, told journalists in Dakar that those who had not been identified by name could lose their right to claim. He was speaking to journalists at the former strongman's appeal case.
Lawyers have said that 4,733 civil plaintiffs were involved in the July case.
Of those, 1,625 were direct victims of regime brutality, having been jailed without trial or taken prisoner of war. Around a dozen women could claim for rape or sexual abuse, they said.
But the victims' main lawyer Jacqueline Moudeina said they were now concerned the judgement made in July risked excluding "thousands of people with the right to compensation."
The criteria required to be identified were difficult to meet for many victims, Moudeina added, including travelling to Chad's capital, N'Djamena, to be interviewed.
"The criteria required by the chamber for compensation are outside the bounds of international legal practices," lawyer Houssine added, appealing for flexibility given the International Criminal Court's less rigorous requirements in similar cases, he said.
The July verdict followed the May sentencing of Habre to life for war crimes and crimes against humanity, bringing closure for relatives of up to 40,000 people killed and many more kidnapped, raped or tortured.