"Member states can not let selected companies pay less taxes by allowing them to artificially shift their profits elsewhere", she said in the Commission's press statement.
The Ikea inquiry is the latest in series of investigations by European regulators since 2013 into the tax structures of multinational companies operating in Europe and how they are treated by the local tax authorities.
The Commission said Dutch-based Inter Ikea, one of the Swedish giant's two divisions, may have been given unfair tax advantages by the Netherlands. Inter-Ikea Holding holds the trademark rights to Ikea and, like the Ikea Group owns a foundation.
The European Union has announced an investigation into the tax model used by Ikea.
"The Commission has concerns that two [Dutch] tax rulings may have given Inter Ikea Systems an unfair advantage compared to other companies", it said.
The commission has already trained its sights on Netherlands's tax rulings in the past. The Dutch subsidiary financed the acquisition by taking out a loan from its Liechtenstein parent. However, the Swedish company claims that several points of the report are mistaken, but this will not stop the European Commission from clarifying whether Ikea may have received illegal state aid in the Netherlands.
The EU said the 2006 tax ruling endorsed a method to calculate an annual license fee that Inter IKEA Systems in the Netherlands paid to another IKEA company called I.I. Holding, based in Luxembourg.
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European competition commissioner Margrethe Vestager said: 'Countries can not just allow selected companies to pay less tax.
Earlier this month the EU General Court rejected an application by the USA government to intervene in the Apple state aid case, concluding that the U.S. did not have a sufficient interest in the result of the case. It also endorsed the interest to be paid under loan to the parent company and the deduction of these interest payments from Systems' taxable profits in the Netherlands.
"As a result of the interest payments, a significant part of Inter IKEA Systems' franchise profits after 2011 was shifted to its parent in Liechtenstein".
The Commission's investigation concerns the tax treatment of Inter IKEA Systems in the Netherlands since 2006. In October, the Commission referred Ireland to the European Court of Justice for not recovering illegal tax benefits from Appleworth up to €13 billion (more than 15 billion dollars).
I.I. Holding paid no corporate tax in Luxembourg because of Luxembourg tax rules in place at the time.
Under EU law, governments can not give businesses selective tax benefits that are not available to other firms. It says it will be looking in particular at whether the level of the annual licence fee paid from 2006 to 2011 reflected Systems' contribution to the franchise business.
The commission said it believed the tax treatment given to IKEA wasn't available to other companies in the Netherlands.