His death was announced on Chadian state television but has not been confirmed by other sources.
Mokhtar Belmokhtar is a former al-Qaeda leader said to have ordered January's attack on an Algerian gas plant where at least 37 hostages were killed.
Chadian troops are fighting Islamist militants in Mali as part of an international force led by France.
"Chadian forces in Mali completely destroyed the main jihadist base in the Adrar de Ifhogas mountains... killing several terrorists including leader Mokhtar Belmokhtar," the army statement on Chadian TV said.
Weapons, equipment and 60 vehicles were seized, it added.
If confirmed, the death would be a major blow to Islamist militants in Mali, the BBC's West Africa correspondent Thomas Fessy says.
'Final stages' Reports of the killing came a day after Chadian President Idriss Deby said the country's forces killed al-Qaeda militant Abdelhamid Abou Zeid during clashes in northern Mali.
Abou Zeid - whose death is still to be confirmed by DNA evidence - is said to be second-in-command of al-Qaeda in the Islamic Maghreb (AQIM), which is fighting foreign forces in Mali.
The French military - which is leading the military offensive in northern Mali - has not confirmed either death.
On Friday French President Francois Hollande said the operation was in its final stages.
Islamist militants took refuge in the remote mountains in northern Mali, close to the Algerian border, after being forced out of the main towns and cities by French troops backed by jets and helicopters.
Mali's army and troops from several African countries have also been involved in the fighting.
Islamist rebels took control of northern Mali a year ago after a military coup in the capital Bamako, in the south.
France intervened militarily in January amid fears they were preparing to advance on Bamako. 'Mr Marlboro' Algerian-born Mokhtar Belmokhtar has been fighting as an Islamist militant for more than two decades.
He claimed to have received military training in Afghanistan before returning to Algeria, where he lost an eye fighting in the Islamist insurgency in the 1990s.
He then joined AQIM - which operates across the Sahara - before breaking off to lead his own group.
The attack on the In Amenas gas plant in Algeria - which he claims he was behind - was his group's first large-scale armed attack.
He is also known as "Mr Marlboro" because of his alleged role in cigarette smuggling in the region.
Mokhtar Belmokhtar and Abu Zeid have also been involved in numerous kidnappings.
If confirmed, their deaths raise concerns about the fate of several foreign hostages believed to be in their power, our correspondent says.