Dagestan Deputy Prime Minister Amutshi Amutinov and Security Council Secretary Akhmednabi Magdigadyev were unhurt by the blast in the northern city of Kizlyar on Wednesday, according to a spokesperson for Dagestan Interior Minister Dmitri Nikiforov.
The booby-trapped car, parked in front of the Kizlyar administrative district, exploded as a Mercedes carrying the two government ministers passed by.
"Following the explosion, eight people were wounded, three of whom died," Nikiforov said.
According to ITAR-TASS news agency, the attack was the fourth assassination attempt on the deputy prime minister.
Dagestan Deputy Interior Minister Magomed Omarov and two of his bodyguards were killed on 2 February when their car was sprayed with bullets in the capital Makhachkala.
Dagestan is an ethnically mixed republic between war-torn Chechnya to the west and the Caspian Sea to the east.
Since 1999 it has been the scene of numerous attacks attributed to separatist groups infiltrating from breakaway Chechnya.