GST reimbursement in works contracts remains contractual, but statutory return, interest and limitation rules cannot be overridden.

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....Contractual claims for reimbursement of GST in post-GST works contracts arise from the agreement between contractor and employer, but they do not alter the statutory scheme for levy, assessment, recovery and enforcement of GST. Any reimbursement direction operates only against the employer under the contract and cannot be enforced against tax authorities or the State. The statutory GST framework also cannot be bypassed through directions permitting revised returns contrary to the Act, or by granting waiver of statutory interest and penalty, or relaxation of the prescribed limitation for returns and revised returns. The impugned order was therefore confined to the contractual reimbursement issue and set aside to the extent it conflicted with GST law.....