One officer was also killed in the clash in Gorno-Badakhshan province, which borders Afghanistan and China.
The ministry said some 200 members of what it called organised criminal groups had blocked a road linking Tajikistan and China to "destabilise the social and political situation".
The same groups attacked a security convoy with firearms and petrol bombs, the ministry said, killing the officer and wounding 13 other troops. Security forces killed eight attackers and detained more than 70 people.
The ministry said order has been restored in the province where protesters have demanded the resignation of the provincial government appointed by President Emomali Rakhmon.
Rakhmon has been in power since 1994, gradually consolidating power and sidelining political rivals and opposition groups.
The operation followed clashes last year between protesters and security forces in the provincial capital Khorog in which at least one protester was killed by police..
Dozens of people were killed in fighting between a domestic armed group and government forces in Gorno-Badakhshan in 2012 and in the 1990s, when the province, whose population is ethnically different from the rest of Tajikistan tried to gain independence from Dushanbe.
(Reporting by Nazarali PirnazarovWriting by Olzhas Auyezov;Editing by Robert Birsel and Angus MacSwan)
