All three deaths were in Pattani, the ministry said.
M79 grenades and other explosions hit 15 spots in Muang district of Pattani and bombs exploded in three locations in Rueso district of Narathiwat, according to security authorities. All took place around 7.30pm.
A navy partol ship was damaged after one of the three bombs hit the vessel on the Pattani River.
The injury toll was 55 on Saturday night, but rose to 73 on Sunday.
Col Pramote Prom-in, spokesman for the Internal Security Operations Command Region 4, said on Sunday the situation was under control.