"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 EU's competition chief has also asked Apple to provide details of its latest tax structure as regulators try to recover €13bn (£11.5bn) in back taxes to Ireland.
Inter IKEA Systems B.V., the Dutch company at the heart of the investigation, said in a statement: "Inter IKEA Group including its subsidiary Inter IKEA Systems B.V.is committed to paying taxes in accordance with laws and regulations wherever we operate".
The first concerned the acceptance of a method in 2006 to calculate an annual licence fee to be paid to another company of the Inter Ikea group, based in Luxembourg. The money has allegedly been illegally shifted to Luxembourg and Liechtenstein, where IKEA pays less or no tax.
Under scrutiny are two Dutch tax rulings that may have given Inter Ikea, one of the Swedish corporate giant's divisions, unfair tax advantages that "have significantly reduced" the firm's taxable profits, BBC reported.
They'll also review a 2011 tax ruling on the reorganization of the company's tax affairs, looking at whether the price Inter Ikea Systems agreed on to buy intellectual property rights and the interest paid on an intercompany loan reflect economic reality.
In a similar Dutch case, the European Union decided against coffee-shop chain Starbucks in the Netherlands and ordered the latte and espresso-maker to pay roughly 30 million euros in back taxes.
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European Commission opens "in-depth" investigation into IKEA's tax affairs in Europe. She's already ordered Apple Inc., Starbucks Corp. and Amazon.com Inc.to repay tax while a probe of McDonald's Corp.is continuing.
European Competition Commissioner Margrethe Vestager said all firms "big or small, multinational or not, should pay their fair share of tax".
Ikea also negotiated a deal in 2006 with the tax service allowing it to transfer a significant portion of its profits to Luxembourg, where it is not required to pay tax. 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.
I.I. Holding paid no corporate tax in Luxembourg because of Luxembourg tax rules in place at the time.
The role of EU State aid control is to ensure that Member States do not give selected companies a better tax treatment than others, via tax rulings or otherwise.
Inter IKEA's subsidiary, Inter IKEA Systems, recognizes significant income in the Netherlands. Regulators will assess "if the level of the annual license fee reflects" the company's 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.