Italy granted permission for 105 migrants rescued at sea to transfer to a sturdier boat, after more than a daylong bureaucratic tussle left them exposed to the elements.
Even more migrants risk falling into bureaucratic limbo amid mounting tensions between EU countries as the bloc seeks to avoid another migrant crisis this summer.
Last week the EU outlined how it would tackle the issue.
"We all agree that we have to better protect our external borders even more", said EU Migration Commissioner Dimitris Avramopoulos.
"We want to expand and beef up the European borders and coastguard and have a fully integrated European border management system."
By June the EU is hoping to reform the current Dublin system.
Under this system a refugee must register in the first EU country they enter and cannot seek asylum somewhere else for a period of six months.
One proposal is to extend that deadline to ten years.
The new proposal would also seek to impose quotas only if refugee numbers spike.
But Hungary said it won't accept any migrants, and Prime Minister Orban will push through a constitutional amendment to this effect.
On a radio programme he said: "We feel we are morally obliged to carry out the amendment of the constitution now."
The EU is acutely aware it must avoid another crisis as it would fuel support for populist parties aligned against migration.