"Europe needs a binding and permanent system for relocating refugees," European Parliament President Martin Schultz told EU leaders at the beginning of the summit in Brussels.
But Spain rejected the plan, along with Hungary, Poland, Slovakia and the Czech Republic, reported Spanish news agency Efe.
The meeting, attended by Spanish Prime Minister Mariano Rajoy, was the fourth EU summit this year on the refugee crisis.
A group shot of the EU leaders attending the summit. Photo: John Thys/AFP
Germany and the European commission were keen to implement a new asylum and immigration system with the aim of sharing migrants across the EU on a permanent basis and German Chancellor Angela Merkel spoke of "sharing the burden" during the summit.
Germany asked for a "small reference" of support for the measures proposed by the European Commission in September (which includes the permanent refugee settling plan) to be included in the concluding text, according to the Spanish Huffington Post.
But the idea was rejected by Spain, as well as by Hungary, Poland, Slovakia and the Czech Republic, which make up the Visegrad group, an alliance of the four central European states.
Spanish Prime Minister seemed upbeat after the summit, tweeting about the EU leaders’ plan to provide more help to Turkey to deal with the refugee crisis.
Hay que acabar con este drama humanitario, ayudar a Turquía que recibe millones de refugiados y normalizar la situación Libia y Siria #EUCO— Mariano Rajoy Brey (@marianorajoy) October 15, 2015
"We need to end this humanitarian drama, helping Turkey, which receives millions of refugees and normalizing the situation in Libya and Syria."
The EU struck a deal with Turkey to help stem the flow of refugees into Europe, providing a multimillion euro package to halt people smugglers and stop refugees fleeing Syria from crossing the sea to Europe.
Rajoy asked for the debate on permanent and binding quotas to be postponed to allow Spain to concentrate on the “provisional” quotas it agreed to in September, according to Europa Press.
Spain has already agreed to accept 14,931 refugees under a quota scheme devised by the EU in early September.
Around 78 percent of Spaniards are in favour of the implementation of obligatory refugee quotas according to a Eurobarometer study released on Thursday.