The ambush targeted five police vehicles driving through the mountainous Tsumadinsky district on a special operation against suspected rebels, a statement said, adding that it occurred just after midnight.
"Unidentified attackers triggered an explosive device and shot at the motorcade," the ministry said. Two police officers died at the scene and three were hospitalised with gunshot wounds.
A spokesman for Dagestan's interior ministry told the Interfax news agency that the police cars triggered a landmine in the remote district before attackers opened automatic gunfire.
The deaths came after four officers died from gunshot wounds while carrying out a police special operation in the district on Monday and seven were hospitalised, the ministry said.