The Center for Political Beauty (ZPS) on Monday installed a transparent urn, which it claimed contained the remains of Holocaust victims.
The ZPS said the urn contained remains recovered from dams, rivers and fields near former Nazi camps in Germany and what was Nazi-occupied Poland.
The art installation, intended to raise awareness of right-wing extremism, received criticism from religious leaders and memorial organizations.
"Auschwitz survivors are dismayed that this memorial violates their feelings and the eternal peace of their murdered relatives," Christoph Heubner, executive vice president of the International Auschwitz Committee, said in a statement.
"The idea that the ashes of their murdered family members will be transported through Europe for demonstrations is difficult for them to bear. Even if they understand and respect the political intentions of the initiators, they consider this kind of demonstration to be impious," he added.
In a statement published online, the ZPS group said it will now cover the urn, which was originally transparent.
"We sincerely regret that we did not recognize the central impact aspect of our work in advance. When we began to visit the places where we suspected the remains of the murdered were, we were overwhelmed by the horror," the group said in a statement.