Reg : TDS deducted on Inv amount

Hi sir,

one of my colleague had a govt. client, where my colleague recognized Taxable value as income in books as per invoices, but govt. client deducted TDS on invoice value in that year, by this 26AS income is more than books as per IT department concern.
finally department issued 139(9) notice of defective return due to turnover difference...
how should I reply to department with proper reason...
is there any rule to govt. to deduct TDS on Invoice amount?
Please help in this regard...