A week ago Benedict lifted the excommunications of four traditionalist bishops, including Richard Williamson, a Briton who denies the full extent of the Holocaust, to try to heal a 20-year-old schism in the Church.
Vatican sources and officials have said the decision was taken without wide consultation within the Vatican or beyond.
"This and other controversies point to a fatal systemic flaw in the Benedict papacy that is destroying his effectiveness as pope: He does not consult experts who might challenge his views and inclinations," said Father Tom Reese, senior fellow at the Woodstock Theological Center at Georgetown University.
"He is surrounded by people who are not as smart as he is and who would never think of questioning him. A smart man surrounded by less than smart people will always get in more trouble than an average man who consults smart people who are experts in their fields," said Reese, a leading US Jesuit.
One man the pope did not consult was Cardinal Walter Kasper, head of the Vatican office on Christian unity Jewish relations.
To many it seemed like a replay of 2006 when Muslims criticised a papal speech in Germany, seen as equating Islam with violence. Benedict did not consult widely before making it.
Williamson told Swedish television in an interview broadcast on January 21: "I believe there were no gas chambers". He said no more than 300,000 Jews perished in Nazi concentration camps, rather than the 6 million accepted by mainstream historians.
Among those who condemned Williamson and the pope's decision to rehabilitate him were Holocaust survivors, Catholics, Israel's Chief Rabbinate and the Jewish writer and Nobel Peace Prize winner Elie Wiesel.
Williamson later posted on his blog a letter apologising to the pope for the "unnecessary distress" he caused him but he did not take back the comments, which he called "imprudent".
"Sham apology"
Abe Foxman, director of the Anti-Defamation League in the United States: "This is a sham apology ... Just to say he is sorry that he made the pope look bad does not solve it. He stands by his bigotry. He should recant what he said."
"His apology for embarrassing the pope is beside the essential point of our concern if he has not apologised for and recanted his comments," said Rabbi David Rosen, head of inter-religious dialogue for the American Jewish Committee.
Elan Steinberg, vice president of the American Gathering of Holocaust Survivors and their Descendants, said: "We still await a proper response from the Vatican."
The controversy has led many to take a closer look at the traditionalist group, the Society of Saint Pius X (SSPX), its view of Jews and its future place in the Church.
SSPX leaders deny it is anti-Semitic but critics point to statements by members they say undermines that assertion.
The US Jesuit weekly America pointed out that the following phrase was on the SSPX's US website a week after the row: "Judaism is inimical to all nations in general, and in a special manner to Christian nations."
Last week one SSPX priest in Italy said gas chambers were used "at least for disinfecting" and another called Pope John Paul heretical because he greatly enhanced Catholic-Jewish ties.
Reese said: "The problem with responding to Holocaust deniers is that it is not clear whether they are just stupid or also anti-Semitic. Stupid people can be educated; anti-Semites need a conversion of heart."
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(Source: TVNZ )