The "Train of Commemoration" traces the plight of 12,000 Jewish children deported to the Auschwitz death camp, often crammed in cattle trucks, between 1942 and 1944.
The exhibit was due to travel to other stations in Germany and arrive at the site of Auschwitz May 8 for the anniversary marking the end of World War II in Europe.
The train will not however stop at Berlin's gleaming new Hauptbahnhof main train station, after being blocked from doing so by state rail operator Deutsche Bahn, according to organizers.
Deutsche Bahn initially refused to let the exhibition be shown at any German stations arguing it deserved more than the divided attention of hurried commuters.
The rail operator relented after its stance drew strong criticism but it has nonetheless come under fire for charging the organisers transport fees.
Michael Szentei-Heise, a Jewish community leader in Duesseldorf, has called Deutsche Bahn chief Hartmut Mehdorn "a Nazi at heart ... (who) would have arranged the deportation of Jews with great conviction."
On Saturday evening, several hundred people carrying candles and placards with the names of people deported took part in a silent march in front of Berlin's Brandenburg Gate.