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For claiming the Cenvat Credit, you have to maintain separate accounts for receipt, consumption of the inventory used for exempted goods and dutiable services (Output Service).
If not then he can follow any of the 2 options
1. Pay Excise Duty on entire exempted goods @ 5%.
2. Pay an equivalent amount of Cenvat Credit attributable to the exempted goods.
Refer Rule 6, of the Cenvat Credit Rules, 2004
since you are providing taxable services and also manufacturing exempt goods, so you will fall under Rule 6(3) of the CCR'04.
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