All parties agreed to receive 20,000 refugees who are currently not in EU territory, mainly in countries like Lebanon or Jordan. That group and a few thousands more, a total 22,500, will be accepted in different European nations.
But several countries refused to take a share of the 40,000 asylum seekers who are currently in Greece and Italy.
"It's a partial victory and a partial failure. Some countries which could have taken a bigger responsibility won't do it," Swedish Justice Minister Morgan Johansson tells Swedish Radio News.
Hungary chose to stay out of the deal and some large countries like Spain and Poland said they would not accept all the refugees the European Commission had suggested.
"Sweden has taken its responsibility. Now it's once again up to those countries who haven't done so to show that they're ready to take their responsibility," Johansson adds.
The EU Commission had suggested a system which would force member states to accept refugees according to a distribution method. Sweden will receive 1,860 people, following the EU's expectations, but many other countries refuse to accept orders from the Commission and demand an optional system where every nation gets to decide.
EU Commissioner for Migration and Home Affairs Dimitris Avramopoulos is disappointed.
"Member states must keep their promises about receiveing 40,000 people from Greece and Italy. I'm disappointed we didn't get there today. Optional systems have been a failure whenever they've been tried," Avramopoulos says.
The most reluctant countries are in Eastern Europe, and have failed to meet other EU' expectations. Germany, France and Sweden have already accepted many asylum seekers and are willing to receive more.
During the same meeting, the ministers discussed the possibility to declare Kosovo, Albania, Bosnia, Macedonia, Montenegro and Serbia safe countries of origin. The consequence would be that EU countries could automatically dismiss asylum requests from those nations.
The EU is currently receiving more asylum requests from Kosovo, around 50,000, than from war-torn Syria, with some 30,000. Many of those asylum seekers from the Balkans are Roma people who claim they are persecuted in their home countries.
This measure has stirred controversy because it is against international law and critics claim the reasons to include a country on that list are arbitrary, daily Svenska Dagbladet reports.