Medecins Sans Frontieres says plans by Greece for new migrant facilities amount to the creation of detention centres.
Europe is at risk of creating a "lost generation" of young refugees, who aren't properly integrated into their host countries, the EU's Agency for Fundamental Rights warns.
The NGO faces a fine of up to €901,000.
"We are absolutely devastated by this tragedy," MSF wrote on Twitter.
Turkey seized 82 migrants in the coastal town of Ayvacik on Monday after finding them in back of a truck.
While the military mission called Eunavfor Med - Operation Sophia (ENFM) is in charge of training and evaluating LCG, its staff is not permitted to set foot in the country due to security conditions.
More than a dozen people have died after a crowded boat carrying migrants capsized in the Mediterranean late on Sunday.
The UN agency has been accused of being a “fig leaf” for the policy of externalisation of EU borders; critics argue that UNHCR action is Libya is uneffective. We asked migrants held in detention centres their opinion.
A video released by Markus Rinderspacher, the Bavarian state parliament vice-president, shows the tense exchange between the mission-Lifeline captain and the port authorities in Pozzallo.
Syrian man given 9.5-year jail term over deadly stabbing in Chemnitz