On September 1950, Toepfer received a coded request for a private meeting with the brother of Hartmann Lauterbacher, a former SS Major-General, former deputy head of the Hitler Youth and gauleiter. Toepfer had known him since the mid-1930s. In 1950, Lauterbacher was in hiding, having escaped from Italian custody. His brother evidently requested that Toepfer contact an associate in Buenos Aires requesting him to help Lauterbacher and his "large circle of friends" to set up a new life in Argentina. A copy of Toepfer's letter of recommendation, dated 2 October 1950, survives in the Alfred Toepfer Archive.

Toepfer with British Prime Minister Edward Heath in 1972 when Heath was awarded the Toepfer-funded European Prize for Statesmanship 

Lauterbacher boarded a ship to Buenos Aires a few weeks later, following the same route taken by Adolf Eichmann during the same year. Subsequent reports identify Lauterbacher as one of the main organisers, together with Otto Skorzeny, of Die Spinne (The Spider), the escape organisation for members of Odessa (Organisation der ehemaligen SS-Angehörigen, that is Organisation of Former Members of the SS). Evidently, Lauterbacher was more concerned to develop the Argentina ratline for other wanted Nazi officers than for himself. He was soon in Egypt where he was reportedly part of a group of Nazis sent, with the connivance of the CIA and West German intelligence, to train anti-Israel guerrillas. 

Toepfer gave financial help and support to many other Nazis, whom he considered as victims of Allied — especially British — brutality. He complained repeatedly about his own prewar internment by the British and about the fact that he had been questioned by a "Jewish officer", though there is no evidence that he was in any way ill treated. He helped to fund SS Lieutenant-General Werner Lorenz's defence before the US military tribunal in Nuremberg. He entertained and assisted SS Lieutenant-General Werner Best. Apart from his senior role in the Gestapo, Best had participated in thousands of murders in Poland and had been Germany's plenipotentiary in occupied Denmark. Soon after his release, Best was implicated, along with Veesenmayer, in a neo-Nazi plot uncovered in 1953 by the British occupying authorities.Toepfer offered employment to SS Colonel Hermann Bickler while he was on the run from the French, who had sentenced him to death. He awarded prizes to the former Nazi rectors of Hamburg and Freiburg Universities (both prewar board members). The list of favours to Nazis and acts of support to far-Right causes is almost endless.

Even Toepfer's seemingly innocent farming and environmental activities had a völkisch dimension. As head of the Nature Park Society from December 1953, he orchestrated protests against the British forces using Lüneburg Heath as a military training ground. The heath, scene of the German surrender in 1945, was a place of nationalistic pilgrimage.

Toepfer's attachment to the "Blood and Soil" philosophy of working the national land provides the background to a controversy about his reported relationship with the Holocaust denier Thies Christophersen. This former concentration camp guard, far-Right farming mystic and author of The Auschwitz Lie, who died in 1997, claimed that he had received funding from Toepfer but that this had ceased when he wrote his book. The Alfred Toepfer Foundation points out there is no evidence for this apart from Christophersen's own testimony.

It took many years for doubts about Toepfer's self-proclaimed anti-Nazism to emerge. Critical material appeared in a German dissertation published in 1973. In 1978, American doctoral research cast light (based partly on French war crimes trials) on Toepfer's subversive pre-war role in Alsace-Lorraine.

In 1979, the award of the European Prize for Statesmanship to French Prime Minister Raymond Barre attracted ridicule in the satirical magazine Le Canard enchaîné, which portrayed the money attached to the prize as comparable to the gift of diamonds to President Valéry Giscard d'Estaing by Emperor Bokassa of the Central African Republic.