The EU is taking Ireland to court over its failure to recover up to €13bn in illegal state aid from tech giant Apple.
Ireland was ordered to recover the money after the commissioner said last August that the country had allowed Apple to "pay substantially less tax than other businesses".
It said Apple's tax arrangement had enabled one subsidiary, Apple Sales International, to pay 0.005% tax in 2014 - just £50 in taxes on every £1m of profit.
The probe found profits were routed via Ireland to virtual head offices that had no employees, no premises and carried out no real activities.
These profits were not subject to tax in any country under provisions of Irish law no longer in force.
The commissioner, Margrethe Vestager, said on Wednesday: "More than one year after the commission adopted this decision, Ireland has still not recovered the money, also not in part.
Amazon has also been ordered to pay pay millions over its Luxembourg tax arrangements
"We of course understand that recovery in certain cases may be more complex than in others, and we are always ready to assist.
"But member states need to make sufficient progress to restore competition."
The commissioner said the deadline to recover the money was 3 January 2017, but that Ireland was still working out the exact amount illegally paid to Apple.
It will now be referred to the European Court of Justice.
Apple has had a base in Cork since 1980 and employs around 6,000 people in Ireland.
The sum to be paid by Apple is 40 times bigger than any previous demand in such a case.
The Irish government called the commissioner's decision "wholly unnecessary" and that it does not accept its analysis of Apple's tax arrangements.
Apple chief executive Tim Cook said last year that the ruling would have a "profound and harmful effect" on investment and job creation in Europe and that the company paid all the taxes it owed in all the countries where it operated.
The decision comes as the European Commission also ordered Amazon to pay around €250m (£220m) in back taxes after finding it had benefited from an illegal tax state aid deal with Luxembourg.