In the letter the NGO calls on EU leaders to guarantee the principle of "non-refoulement", that the refugees won't be sent back to a war zone.
Speaking to Radio Sweden, the head of the Swedish branch of Doctors Without Borders, Kristina Bolme Kühn, says that Swedish Prime Minister Fredrik Reinfeldt has a responsibility to discuss the issue with the other EU leaders.
"We feel there are double standards in the current political cynicism," she says, "you engage in a conflict on humanitarian principles, and then when it comes to the civilians that are fleeing the war there are obstacles, or an unwillingness to take care off these people when they try to reach our borders."
Doctors Without Borders are on the ground trying to help the refugees on the tiny Italian island of Lampedusa, and conditions there are grim says Bolm Kühn.
"Twelve thousand people coming more or less at the same time is an enormous burden for the island", she says, "(the refugees) come exhausted and shocked. Some of them are even very sick. There is not enough space to take care of them, for example, they are forced to sleep outside, the centres are overcrowded. A lot of these people come from Libya because they are already migrating from other parts of Africa, for example, and then the war hits and then they are fleeing again. So they are traumatised by previous bad conditions, and now they are coming to a Europe that is not giving them a warm welcome, but rather a cold hand."