Tonnage tax option requires application to the Joint Commissioner with written approval or refusal within prescribed timeframes.

A qualifying company may opt into the tonnage tax scheme by applying to the Joint Commissioner in the prescribed form. Existing companies could apply during an initial period; other qualifying companies must apply within three months of incorporation or of becoming qualifying, and an IFSC unit losing section 80LA deduction may apply within three months of cessation. The Joint Commissioner may seek information, and must pass a written order approving or refusing the option after giving a reasonable opportunity of hearing; approval takes effect from the assessment year relevant to the previous year in which the option is exercised.

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