The attack targeted the church where prayers of Christian community were being held, the Express Tribune newspaper reported quoting Balochistans Home Minister Sarfaraz Bugti.
A loud explosion and gunshots were heard, it said.
The paper said that at least two people were killed.
According to eyewitnesses, a number of people have sustained injuries.
Following the attack, an emergency was imposed in all hospitals across Quetta.
Police teams and rescue teams have reached the site of the explosion, and the area has been cordoned off.