Tds on vat portion

Deepthi Srivastava (Chartered Accountant) (81 Points)

31 October 2012  

Hello,

I need to know if TDS can be deducted on VAT portion as well. 

We work for the Govt organisations (defence). We are required to raise 2 bills.. one for the material amount and second for the VAT amount. The VAT amount is paid on actual basis i.e. it a reimbursement after the VAT is actually paid. 
Our customer is deducting TDS on Both the bills under sec 194C. 

I do not understand why TDS is being deducted on VAT portion. We only collect and pay it to the government. Where is income portion in this? Plus in our case, we pay first and then get reimbursed for VAT. I tried looking for answers in the APVAT Act, but couldn't find any solution. 

Please reply with relevant refernce to a section/notification.