Question1:

If a GST officer of the rank Assistant Commissioner confirms the demand under Section 129(3) in a seizure case. The tax payers wants to contest, but deposits the amount under protest for release of goods. Whether the tax payer can file appeal before the authority against the order or the order shall be treated conclusive under Section 129(5) for depositing the tax and penalty?

Answer

According to provisions of Section 107(1) of CGST Act, 2017 read with Rule 108(1) of CGST rules, 2017, appeal can be filed, if aggrieved,  against any adjudication order passed by an officer of the rank of Assistant Commissioner before an appellate authority of the rank of Additional Commissioner. 
Since you are aggrieved against the adjudication order mentioned in your quarry, you should file appeal for redressal of you grievance. (Reply dt. 12/3/2018)