Rahimov rejected reports about the existence of a "blacklist" to prosecute alleged participants in recent clashes between security forces and police.
A special operation conducted in July by security forces in the eastern Gorno-Badakhshan province left some 70 people dead.
Clashes between troops and militants, fuelled by the killing of a local security chief, lasted until late August.
Local citizens claim the majority of those killed in the clashes were ordinary people, not militants.
Last week, Tajik President Emomali Rahmon on a visit to the restive region said there would be "no more talks with militants."