The operation by both the army and police follows yesterday attacks that saw eight policemen and nine militants killed and which the government said were orchestrated by former deputy defence minister Abduhalim Nazarzoda.
"At this time, 32 members of Nazarzoda's criminal group have been detained, 13 of whom have been eliminated," the ministry said in a statement.
Four policemen were killed in a shootout with militants on the outskirts of the capital Dushanbe yesterday and another four officers were killed in an attack in the town of Vahdat just outside the capital, the interior ministry said.
More than 500 weapons and ammunition have been seized from group during the operation, authorities said.
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The government has said that 51-year-old Nazarzoda - relieved of his duties yesterday "in connection with a crime committed" - fought on the side of the United Tajik Opposition during a civil war that lasted between 1992 to 1997.
Authorities have also claimed that the former deputy defence minister was a member of the opposition Islamic Renaissance Party of Tajikistan (IRPT) that the government effectively shut down last week.
Nazarzoda and up to eight of his accomplices have fled to the mountains northeast of the capital, the ministry said.
Authorities have launched a massive air and ground search operation in the area, dispatching military helicopters and additional army units.
Nazarzoda - who had served as deputy defence minister since last January - had worked at the ministry since 1999, when anti-government fighters were integrated into state institutions after the civil war.