In 1993, 1996 and 1999 a series of protests led to the abandonment of annual prizes administered through the Universities of Vienna and Strasbourg, the cancellation of an award ceremony at the French Senate, questions in the Swiss cantonal parliament in Basle and, in 2000, the abandonment of the Robert Schuman Prize. 

During his life, Toepfer reacted to the occasional protests against him by consulting lawyers and by issuing brazenly inaccurate accounts of his personal history. 

In 1996, three years after his death and after the debacles in Strasbourg as well as a powerful series of articles by French writers and academics led by Lionel Boissou, the Alfred Toepfer Foundation decided that simple denial would no longer suffice. It employed the public relations firm Goerres and Partner and then created an "Independent Academic Commission" to produce a credible history. Its lead historian, Professor Hans Mommsen, wrote to the Toepfer Foundation that its researches would take the "wind out of the sails" of the critics.

The three years during which the commission conducted its work coincided with attacks by young German historians on their predecessors. They produced evidence to show that some leading post-war German historians had been active under Hitler in advocating and planning "dejudaisation" in Eastern Europe. The conflict came to a head at the annual conference of German historians in 1998. Some of the historians now exposed, such as Theodor Schieder, had been part of Toepfer's network of boards and committees during the Hitler period. The controversy over Toepfer's past thus became a symbol of the wider debate about the cover-ups which, according to such younger historians as Ingo Haar and Michael Fahlbusch, had pervaded the German historical profession after 1945. 

When the 488-page report of the Toepfer Foundation's historians appeared in 2000, it fulfilled many of the critics' fears. Purporting to present a balanced judgment and including qualified admissions, it could be viewed, as one of the junior authors (himself not a member of the commission) recently testified, as a PR exercise. As with similar histories financed by companies with controversial records of activity under the Nazis, some of the most damaging facts about Toepfer were buried in obscure parts of a turgid tome or given cursory treatment. The introductory summary (the only part of the book translated into English and carried on the foundation's website) mentioned that Alfred Toepfer employed Veesenmayer and Haller after the war, but only in a footnote. The sympathetic headline conclusions in this introduction did not follow from the evidence. 

The lead authors claimed that Toepfer was neither anti-Semitic nor racist, failing to explain why so many of his colleagues were both of these things and why he promoted the Nazi agenda. The history stressed that Toepfer was not a member of the Nazi party, assuming that this single piece of evidence proved that he was not a Nazi. Key documents and areas of research were ignored. A paean for Nazism which Toepfer published in 1940 was not set before the reader. It included the following passage: 

"National Socialism has not only permitted social justice in Germany, it has achieved it. National Socialism has not only promised an end to unemployment and the economic misery of the masses, it has achieved both these things. National Socialism has not only promised to youth and to the Volk, irrespective of birth or wealth, a life-embracing education, both for body and mind, it has achieved this. Thanks to National Socialism we now have Völkisch [racial] unity, political leadership and the formation of a general political will; we have a concentration of power without equal in German history."