What are you feeding your puppies ? This could also be due to food allergy. Try to keep your puppies on a commercial diet for atleast 6 months or so, making sure you don't feed grain based food items like roti or bread.
Secondly, this could also be due to some chemical that's being used in your house like Phenol. Please cease the usage of this substance. You can use other more pet friendly substitutes available in the market, like Domex.
Thirdly, get your puppies checked with a Vet who will conduct some tests to rule out the possibility of Scabies mites in your puppies. Dogs can carry these mites from one to another. If the mother is scabies infected, it's inevitable for the puppies to be infected as well.
Lastly, bathe your dogs only when you have to. Use a good grooming brush and dry bath shampoo. You can also start adding supplements in the food to help your dogs recuperate from this problem.