GST transition in works contracts separates contractual reimbursement disputes from statutory assessment, recovery and enforcement obligations.
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....GST liability arising from works contracts spanning the pre-GST and GST regimes must be determined under the applicable statute, while reimbursement of any incremental GST burden depends on the contractor-employer contract. Contractual directions may govern work calculation, representations and GST adjustment, but cannot alter statutory assessment, recovery, interest, penalty, return limitations or enforcement by tax authorities. Assessment orders may be challenged through appropriate proceedings, with the time spent pursuing writ petitions excluded when calculating limitation.....
TaxTMI