Spain's rebate is the result of revised calculations of value-added tax (VAT) and gross national income (GNI), which has prompted Brussels to make financial "adjustments", according to the leaked document published by The Financial Times.
At the other end of the scale, the UK will take the biggest hit, owing €2.1 billion, according to the document, while The Netherlands will have to cough up €642 million in repayments.
The leaked EC document outlines the amounts each country would receive or need to pay, depending on its economic performance since 1995.
"The British economy is growing much faster than the others and the logic is the same as with tax: if someone earns more, they pay more tax," EC spokesman Patrizio Fiorilli told news agency AFP.
"The Commission services are aware that in some cases this might have a significant budgetary impact in terms of cash-flow," the EC note reads.
A senior British source working within the UK's Cabinet Office told the Financial Times: "It is not acceptable to just change the fees for previous years and recover funds on a moment's notice. The EU Commission has not been expecting this money and does not need this money, and we will work together with other countries facing a similar way to change this".