Spain has agreed to take in 14,931 refugees as proposed by the Commission, in addition to 2,749 who were accepted in July, bringing the country's total to 17,680, the source told AFP.
The EU unveiled plans today to take 160,000 refugees from overstretched border states, to ease the pressure from the worst migration crisis since World War II.
The plans call for compulsory quotas for member states, calculated according to a country's GDP, population, jobless rate and number of already-processed asylum applications.
She did not give further details, saying only that the process needed to be "orderly".
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The position appears to be a U-turn by Spain's conservative government.
In July, it resisted the Commission's original proposal, which called for Spain to take a number of refugees that was smaller than under the plan unveiled on Wednesday.
The Spanish government argued at the time that its high unemployment rate of 22.4 per cent and the huge amount of migrants that already reach its southern shores directly from Africa limited its absorption capacity.
Spain like European nations has faced mounting pressure to accept a greater share of refugees, spurred especially by pictures last week of three-year-old Syrian Aylan Kurdi, whose lifeless body washed up on a Turkish beach.