She lashed out as the summit met in Seville to discuss common EU policy on organised crime, human trafficking, mass migration and the threat from Islamic extremists.
Spanish interior minister Juan Ignacio Zoido was joined by his counterparts from the UK, France Germany, Italy and Poland to discuss the threats.
But MEP Marina Albiol hit out at the EU in a Twitter tirade, accusing Brussels of “racism and xenophobia in its purest form” for linking the issues.
She wrote: “The EU is nothing more than a criminal institution at the service of the powerful.
“This has always been like that.
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“It was the way it was conceived.
“In the #CriminalSummit of the G-6 in Seville they link migration with terrorism. Racism and xenophobia in its purest form.
“The EU intends to fight terrorism by persecuting migrants and not by pointing out those who cause wars and support dictatorships.
“Don’t criminalise refugees. Condemn US and EU-led wars in the Middle East.”
She went on: “Seeing that racism and xenophobia are being promoted from European institutions, it is clear that the extreme right has already won.”
Speaking ahead of today’s event, Mr Zoido said the current high level of migration had led to “unprecedented” security challenge for the bloc.
He claimed the joint efforts of southern EU members had successfully stemmed the flow of migration from African coastal nations and the Mediterranean.
But he said more need to be done to build partnerships with the source countries to stop migrants being targeted by criminal gangs.
Alongside migration, the summit is set to discuss the recent terror attacks in the UK, France and Barcelona.
This meeting is a preparation for the EU-African Union summit in November.
(Additional reporting by Maria Ortega)