Deputy Prime Minister Wissanu Krea-ngam on Thursday said the dispute involving Philip Morris, a multinational cigarette and tobacco manufacturing company, is "not over yet".
He made the remarks after the Department of Trade and Industry (DTI) of the Philippines released a statement on its website, which said a World Trade Organisation (WTO) panel has decided to uphold the Philippines' claims that Thailand has been violating international customs law.
Mr Wissanu said on Thursday the Commerce Ministry, the Foreign Ministry, the Customs Department and the Department of Special Investigation are working together to solve the dispute.
He said there are cases being tried in Thai courts, as well as in the WTO court, adding the issue is sensitive and is "not over yet". The company's Thai subsidiary now faces both criminal and civil suits.
The WTO panel issued a ruling on July 12 that Thailand had failed to comply with its obligations under the Customs Valuation Agreement, regarding the valuation of cigarettes imported by Philip Morris Thailand from its subsidiaries in the Philippines.
After the ruling, the tobacco company has urged Thailand to drop criminal prosecution against Philip Morris Thailand Limited (PMTL).
Mr Wissanu said more than 20 letters of protest had been sent to the government after the company called on Thailand to withdraw criminal charges against its Thai subsidiary.
The Office of the Attorney-General charged PMTL with evading taxes by under-declaring the value of cigarettes it imported from the Philippines between 2003 and 2006.
The undervaluation meant that PMTL managed to avoid paying more than 20 billion baht in taxes.