Any taxpayers exempted from paying tax to the dealer/retailer for services/goods?

Ham Joshua (B.Com) (34 Points)

05 August 2018  

We undertaken a works contract of an Educational Institute Under a Charitable Trust who have certificate from Income Tax to exempted from income tax. also they dont want to take any GST registration & collect Tax from their students for their FEES. 

They transferred all funds for our works contact through our bank account. Shall we raise GST bill to them. They were asking tax was not applicable to them so they never pay tax for our service.?

Its very huge amount. its profit is below than 18%. How we pay tax for them. Please help us?