The claim was made by Dr Michael Hesemann, a German historian carrying out research in the Vatican archives for the Pave the Way Foundation, a US-based inter-faith group.
He said that Cardinal Eugenio Pacelli – the future Pius XII – wrote to Catholic archbishops around the world to urge them to apply for visas for “non-Aryan Catholics” and Jewish converts to Christianity who wanted to leave Germany.
Elliot Hershberg, the chairman of the Pave the Way Foundation, said:“ We believe that many Jews who were successful in leaving Europe may not have had any idea that their visas and travel documents were obtained through these Vatican efforts.
“Everything we have found thus far seems to indicate the known negative perception of Pope Pius XII is wrong.”
Pius XII was criticised for failing to denounce explicitly the Holocaust, the Nazi regime or to excommunicate Hitler.
Dr Hesemann says that additional evidence suggests that the visas would have been given to ordinary Jews desperate to escape persecution.
“The fact that this letter speaks of 'converted Jews’ and 'non-Aryan’ Catholics indeed seems to be a cover,” said Dr Hesemann.
“You couldn’t be sure that Nazi agents wouldn’t learn about this initiative,” he said.
“Pacelli had to make sure they didn’t misuse it for their propaganda, that they could not claim that the Church is an ally of the Jews.”
The appeal from Cardinal Pacelli, then the Vatican’s Secretary of State, was dated Nov 30, 1938 – 20 days after Kristallnacht, the “night of broken glass”.
Cardinal Pacelli was able to ask for the visas because the 1933 concordat he signed with the Nazis specifically provided protection for Jews who converted to Christianity.
Dr Ed Kessler, the director of the Cambridge-based Woolf Institute of Abrahamic Faiths, said: “It is clear that Pius XII facilitated the saving of Roman Jews.”
In December, Pope Benedict XVI placed Pius one step closer to sainthood when he declared him “Venerable”, meaning that the Church believes he lived a life of “heroic virtue”.
Two miracles are needed to canonise him as a saint and the Vatican is investigating at least one apparently inexplicable healing.
Some Jewish groups want the process frozen until the Vatican is ready to open its secret wartime archives in 2014.
Sir Martin Gilbert, a British historian and the world’s leading expert on the Holocaust, has said that Pope Pius XII should be considered as a “Righteous Gentile” by Yad Vashem, the Israeli Holocaust remembrance authority.