Speaking at press conference on Friday to unveil the Commission's Spring Economic Forecast, Commission Vice-President for Economic and Monetary Affairs and the Euro Olli Rehn said Spain would be given two more years, or until 2016, to bring the country's public deficit under the European Union's three-percent limit.
Deficit is a crucial measure of financial stability.
The Commission said, however, that Spain's deficit would be higher than the forecasts of the Spanish government in 2013 and 2104.
Rajoy's government have stated that the deficit will be 6.3 percent in 2013 and 7 percent in 2014.
The forecasts from Brussels, however, have these figures at 6.5 percent this year and 7 percent next year.
Brussels also revised down Spain's 'growth' target for 2013.
The Spanish government predicted in February the country's economy would shrink 1.3 percent this year and are now looking at revising this down to 1.4 percent. The European Commission, meanwhile, says this contraction will be 1.5 percent.
The European Commission and the Spanish government do concur on unemployment levels though. Both parties agree the jobless rate will be around 27 percent in 2013 before dropping to close to 26.5 percent in the coming year.
During Friday's press conference, Brussels also announced GDP growth in 2013 was now forecast at -0.1% in the EU and at -0.4% in the eurozone area.
For 2014, economic activity is expected to grow by 1.4% in the EU and 1.2 % in the eurozone area.
Rehn said: "In view of the protracted recession, we must do whatever it takes to overcome the unemployment crisis in Europe. The EU’s policy mix is focused on sustainable growth and job creation. Fiscal consolidation is continuing, but its pace is slowing down. In parallel, structural reforms must be intensified to unlock growth in Europe."