Dublin indicated the the collection was stalled due to negotiations over the escrow account, set to hold the dues while the decision is appealed in court.
Apple may or may not be losing its tax advantage in Ireland, but the company has apparently been exploring other options for tax havens in Europe.
However, last year, the Commission came to the ruling that this is an example of illegal state aid and threatened Apple with harsh consequences if it didn't cough up $13 billion in owed taxes.
The government said in a statement Monday that an agreement had been reached "in relation to the framework of the principles that will govern the escrow arrangements".More news: GST made doing business easier, increased market size for traders: Jaitley
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"We expect the money will begin to be transmitted into the account from Apple across the first quarter of next year", Donohoe said and added that the government was now seeking an investment manager and custodian to operate the fund.
Both Apple and Ireland dragged their feet on the repayment as they appealed the decision in court.
"We have a dedicated team working diligently and expeditiously with Ireland on the process the European Commission has mandated", the company told the Journal in a statement.
Now it appears Apple and Ireland have agreed to cooperate, and pay $15.4 billion to the Irish government, all while however still continuing litigating the case.
Apple believes that the ruling will be overturned in time and that it's acted in accordance with the law.