Sir,
According to Section 140 (6) of the Central Goods and Services Act, 2017-
"A registered person, who was either paying tax at a fixed rate or paying a fixed amount in lieu of the tax payable under the existing law shall be entitled to take, in his electronic credit ledger, credit of eligible duties in respect of inputs held in stock and inputs contained in semi-finished or finished 11[goods held in stock on the appointed day, within such time and in such manner as may be prescribed, subject to] the following conditions, namely:––
(i) such inputs or goods are used or intended to be used for making taxable supplies under this Act;
(ii) the said registered person is not paying tax under section 10;
(iii) the said registered person is eligible for input tax credit on such inputs under this Act;
(iv) the said registered person is in possession of invoice or other prescribed documents evidencing payment of duty under the existing law in respect of inputs; and
(v) such invoices or other prescribed documents were issued not earlier than twelve months immediately preceding the appointed day."
Therefore you are eligible to take credit of inputs and input services utilised in WIP. You may bring this provision to the notice of audit. However, I think the audit objection should be based on some other stronger grounds because I presume the Departmental Officers are aware of this provision.