Exempt items are included in work contracts - how to determine gst

Our Company takes work contracts of construction of transmission line from clients. The item wise pricing details of work contract  contains some exempt items like "land compensation" and "crop compensation".  Our company does not charge GST on such exempt items. While Auditor has objected that work contract is awarded as a whole and not item wise so the whole work contract is taxable 

please give opinion

 

  

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taxable

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