Narathiwat provincial police commander Pol Maj-Gen Chote Chawalwiwat said bomb shrapnel was found and steel shelving was bent from the powerful explosion.
Police believe the bomb was placed on shelving holding flammable products such as hair spray, leading to a quick spread of the blaze.
The authorities are examining surveillance camera images to trace the bombers.
Super Department Store 4 Narathiwat deputy managing director Waraporn Sirichai said damage is estimated at about Bt100 million as the building and goods were totally destroyed.
More than 200 staff are now unemployed as it will take time to rebuild.
Ms Waraporn said she wanted the government to help by extending help such as compensation promptly as her business needed capital to operate and time is needed to recover.