Jose Manuel Garcia-Margallo said he was unhappy with leaving the solution to the crisis in the hands of a country outside the European Union, despite Madrid having backed the controversial deal with Ankara.
"This deal we have signed with Turkey, it's a botched job," he told the Cope radio station.
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"But that does not mean that this is not a botched job, and it leaves the solution in the hands of a third country."
Under the deal, Turkey has agreed to take back migrants landing on Greek islands in exchange for political incentives including billions of euros in aid and visa-free European travel for its citizens.
The Turkish agreement is the cornerstone of the EU's plan to curb a crisis that has seen 1.25 million Syrian, Iraqi, Afghan and other migrants enter since 2015, though the numbers of arrivals have dropped since March.
Garcia-Margallo criticised EU efforts on refugees as "very inadequate" compared to countries like Lebanon, which has taken in more than a million people fleeing the Syrian war -- equivalent to more than a quarter of its own population.
In April, acting Spanish Prime Minister Mariano Rajoy faced heavy criticism from lawmakers over the fact that Spain had taken in only 16 asylum-seekers under an EU relocation plan, out of a promised 16,000.
Garcia-Margallo blamed problems with registering migrants for the slow progress, claiming registration centres in Greece simply "don't work".
"Greece does not have the civil servants to resolve all these problems and the rest of the countries are waiting for someone to tell us 'the process has begun and you must start taking in the refugees'," he said.
He called for a "genuinely shared European asylum agency" to speed up the process.
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