The essential contention raised by the petitioner, is as to the adjustment of the amounts paid on 02.03.2010, by virtue of a conditional order, to the Amnesty Scheme brought into force on 01.04.2010.

2. The petitioner, an assessee under the Kerala General Sales Tax Act, 1963 (for short "KGST Act" only), had dues with respect to the various assessment years from 1998-99 to 2003-04; except 2002-03. The question as to whether the excise duty component can be included in the turnover of the manufacturer was agitated for long years before this Court and the Hon'ble Supreme Court. The decision in State of Kerala v. Maharashtra Distilleries Ltd. [(2005) 11 SCC 1] settled the issue and from 05.01.1999 by virtue of the amendment made to the Foreign Liquor Rules, the Hon'ble Supreme Court held that excise duty was liable to be included in the turnover of the manufacturer. The petitioner/assessee was also a party before the Hon'ble Supreme Court. The assessments made including such component, in the taxable turnover, were challenged in statutory appeals. There was also penalty imposed in the various years, which was challenged by way of revision before the Commissioner.

3. In the appeals against the assessments for the various years, pending before the Tribunal, stay petitions were rejected. The appeals were also finally heard but no orders were passed. Pending disposal of the appeals, recovery was threatened by the Department. Specifically, garnishee proceedings were taken against Andhra Bank, with whom petitioner maintains a current account and the Kerala State Beverages Corporation, who purchases the finished product of the petitioner. The petitioner approached this Court with W.P(C) No.2434/2010, against the garnishee proceedings, which was disposed of by Ext.P1 judgment dated 16.02.2010. This Court in Ext.P1, noticed that the recovery threatened by the Department related to four different components being the tax liability, interest thereon, penalty and interest on penalty. The penalty aspect was not the subject of appeals before the Tribunal and was not agitated in the said writ petition. As to the tax and interest payable thereon, the Court found that only nominal amounts were paid towards the liability. Garnishee proceedings were kept in abeyance on condition of the petitioner depositing a sum of Rs.4,00,00,000/- (Rs. Four crores only) within a period of one week. The Tribunal was directed to pass final orders in the appeals which were heard and reserved for orders. Ext.P1 judgment was on 16.02.2010.

4. The amounts directed to be paid were paid on 02.03.2010 by a Demand Draft. A separate writ petition numbered as W.P(C)No.7918/2010 was filed against the recovery of penalty and interest thereon, since the revisions were pending before the Commissioner and the recovery was stayed till the disposal of the revisions, by Ext.P2 judgment.

5. On 01.04.2010, the Government extended a scheme of amnesty, brought in originally under Section 23B of the KGST Act, by Kerala Finance Act, 2008. The earlier scheme had expired and was afresh made applicable at the inception of the financial year 2010-2011. The scheme offered reduction in interest and penalty for expeditious settlement of dues. The petitioner applied under the scheme. An order was issued at Ext.P4 directing the petitioner to pay Rs.6,66,92,983/- under the amnesty scheme. The order produced at Ext.P4 also showed the adjustment details of Rs.4 crores paid on 02.03.2010. The amounts so paid were apportioned to the interest liability for the various years as provided under Section 55C of the KGST Act. The petitioner then filed Exts.P5 and P6 representations before the Commissioner of Commercial Taxes and the Minister for Finance seeking consideration of Amnesty Scheme without appropriation of Rs.4 crores deposited, prior to the implementation of the scheme and sought for the said amounts, to be adjusted to the dues then, calculated under the amnesty scheme. The above writ petitio