Authorities in Tajikistan say former deputy defence minister Abdukhalim Nazarzoda was among a group of rebels killed on Wednesday.
Gen Nazarzoda was a member of the government until 4 September, when he was blamed for gun battles in which at least nine police officers were killed.
He had since been charged with treason and creating an extremist group.
Tensions between the government and Islamist forces are on the rise in the secular but Muslim-majority state.
The authoritarian government last month effectively banned the Islamic Revival Party, the only legal faith-based party in ex-Soviet Central Asia.
Hiding outGen Nazarzoda was a rebel with the Islamist opposition during the five-year civil war that ended in 1997 with the incorporation of rebels into government under the terms of a peace deal.
But earlier this month gunmen loyal to him clashed with government forces in battles in which police said nine officers had died - prompting President Emomali Rakhmon to vow to take revenge.
Gen Nazarzoda was said to be hiding out at Ramit Gorge with supporters east of the capital Dushanbe.
On Wednesday security forces said they had tracked down and killed him. Reports suggested at least 11 other rebels also died.
Mr Rakhmon has been in power for two decades and was re-elected in 2013 with 83.6% of the vote.
International observers said the election was quiet and peaceful but "without a real choice".
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