You have to charge excise duty based on the following rule 3 of Cenvat Credit Rules, 2004. You have to reduce the excise duty credit taken @ 2.5% per quarter and the balance you have to charge in the invoice.
Basic Value = as agreed by the customer
ED = as per the calculation
VAT/CST = as applicable.
Provided [also] that if the capital goods, on which CENVAT Credit has been taken, are removed after being used, the manufacturer or provider of output services shall pay an amount equal to the CENVAT Credit taken on the said capital goods reduced by the percentage points calculated by straight line method as specified below for each quarter of a year or part thereof from the date of taking the CENVAT Credit, namely :-
(a) for computers and computer peripherals :
for each quarter in the first year @ 10%
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for each quarter in the second year @ 8%
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for each quarter in the third year @ 5%
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for each quarter in the fourth and fifth year @ 1%
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(b) for capital goods, other than computers and computer peripherals @ 2.5% for each quarter.]