Cohen told the weekly Spiegel magazine that he recommended "completely cutting off connections to a body in which Holocaust deniers and anti-Semites are members."
Pope Benedict XVI's pardon of Williamson, along with three other ultra-conservative bishops, has threatened the Vatican's relationship with Jewish leaders and led to an outburst of criticism within the Catholic Church.
Two weeks ago, in an interview with Swedish state television, Williamson said "historical evidence is hugely against 6 million Jews having been deliberately gassed in gas chambers as a deliberate policy of Adolf Hitler."
The timing of Benedict's pardon is considered particularly insensitive, as the announcement came just days before Holocaust Memorial Day on Jan. 27.
The president of Germany's Jewish Central Committee, Charlotte Knobloch, made it clear on Friday that the Vatican's decision weighed heavily on the relationship between Jews and Catholics.
In light of the Pope's German nationality, Knobloch said she would have "hoped for more sensitivity in dealing with the crimes of the National Socialists."
Former Chief Rabbi Israel Meir Lau, a survivor of Buchenwald concentration camp, was quoted in Spiegel asking, "How can such a liar be granted the protection and pardon of the leader of the Catholic Church?"
German Catholics protest
German Catholics have also reacted strongly to Benedict's decision.
In the city of Muenster, where the Pope once taught as a professor of theology, almost the entire Catholic faculty signed a letter of protest, while theologians in the city of Tuebingen described the decision as a "heavy burden".
Swiss theologian Hans Kueng, speaking on German radio RBB, accused Benedict of being out of touch with his "kingdom". In Kueng's words, "the pope has no critical people around him."
In light of this wave of reactions, the Vatican has sought to quell the outrage. During his weekly general audience on Wednesday, Benedict said the memory of the Holocaust cannot be cancelled through any form of denial.
The German-born pontiff also recalled his own past pilgrimages to the former Nazi death camp of Auschwitz. "The images I collected during my numerous visits to Auschwitz bore witness to the innocent victims of a racial hatred," he said.
Questioning the Church?
Spiegel reported that some German Catholics are questioning their adherence to the Church. Helmut Reinhard, a Catholic living in the city of Munich, lost 15 members of his family in Auschwitz-Birkenau, "all of them gypsies," he told the magazine, "and all of them Catholic."
As a result of the Pope's pardon, Reinhard's brother Markus had left the Catholic church, together with his wife and her four sisters, on Holocaust Memorial Day. Now he too has had enough, he told the magazine, and was renouncing his membership.
German public prosecutors have opened an inquiry against Williamson over his remarks. Holocaust denial is a crime in Germany.