Apple and the Irish government had been due to put the money into an escrow account in January but Vestager told Ireland's RTE news that that the deadline has passed. The payment is "complex" and Ireland is still calculating how much is due, she said.
The Commission said in August that Ireland must recover the unpaid taxes from Apple after it concluded that the country granted undue tax benefits to Apple between 2003 and 2014.
"This is illegal under EU state aid rules, because it allowed Apple to pay substantially less tax than other businesses. Ireland must now recover the illegal aid," the Commission said at the time.
The Commission's decision followed a three year investigation into two rulings issued by Ireland in favour of two Apple group companies: Apple Sales International (ASI) and Apple Operations Europe (AOE). These companies were both incorporated in Ireland and, although they did not have any taxable presence in the US or any other tax jurisdiction, they were not treated as Irish tax resident because Irish law at the time regarded them as US tax resident. The Irish law has since been amended and Apple has now changed its operating structure.
The tax rulings concerned the method of allocation of profit to the Irish branches of these companies. The rulings meant that almost all of the sales profits recorded by the two companies were internally attributed to a head office of ASI that the Commission said, in a statement issued in August, "existed only on paper and could not have generated such profits". The profits allocated to the head office were not subject to tax in any country and as a result, the Commission said Apple only paid an effective tax rate of between 0.005% and 1%.
Both Apple and the Irish government are appealing the Commission's decision but had agreed to put the money into the escrow account until the appeals are settled.
The appeals have now been filed "and now it's up to the courts to start the proceedings", Vestager said.
Meanwhile the Commission is working with the Irish authorities and can see that it is making progress on collection of the taxes, Vestager said.
A spokesperson for the Irish Department of Finance said it is "currently engaging with the Commission on the recovery process and we are continuing to make progress on the recovery from Apple with the full cooperation of both the company and the EU Commission."
"The Commission are satisfied with the progress we are making. We have committed to complying with the decision and we fully intend doing that," he said.
Ireland said in December that it believes the Commission has exceeded its powers and interfered with national tax sovereignty, as it attempted to overturn the tax ruling. The Commission had "misunderstood the relevant facts and Irish law", it said.
"Ireland did not give favourable tax treatment to Apple - the full amount of tax was paid in this case and no state aid was provided. Ireland does not do deals with taxpayers," the Irish government said at the time.
The Commission does not have direct authority over national direct tax systems. However, under EU rules it is unlawful for any EU country to give financial help to selected companies in a way which would distort fair competition. If a tax ruling contravenes market principles so as to confer a selective advantage, it could be considered to be state aid.
In June 2014 the European Commission announced in-depth investigations into whether tax rulings issued to Apple by Ireland, Starbucks by the Netherlands and Fiat Finance and Trade by Luxembourg amounted to "unjustifiable" state aid. In October 2014 a similar investigation was announced into Amazon in Luxembourg and in December 2015 an investigation was launched into 'double non-taxation' of McDonalds in Luxembourg.
In October 2015 it decided that the rulings provided to Fiat and Starbucks constituted unlawful state aid and that the countries would have to recover €20-to-€30 million from each company to claw back the benefits of the state aid received. The Amazon and McDonald's investigations are continuing.