In August, the European Commission, the EU executive arm, ordered the iPhone maker to reimburse a record 13 billion euros ($14 billion) in unpaid taxes in Ireland.
The EU had accused Ireland of giving Apple a secret tax deal that allowed it to enjoy near zero tax on its huge sales worldwide for more than a decade.
Addressing Irish lawmakers in Dublin on Tuesday, Vestager denied that Brussels was conducting a "witch-hunt" against multinationals such as Apple.
Vestager said the investigations in this and other cases in other European countries were purely about illegal state aid.
"We simply want to make sure that they are not used to rubber stamp a way of allocating profits that does not match economic reality," she said.
It did not mean that the EU Commission was assuming the authority over a country's tax rules, the commissioner argued.
The investigations "do not affect the sovereign right of member states to determine their own corporate tax systems, or to set their own tax rates. They are simply about special treatment for certain companies," she said.
Vestager said "good progress" was being made by the Irish authorities with regards to the collection of the money.
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