An article, titled "To Strike at the Church of Pius XII" and written by historian Anna Foa, said the decision to re-classify Giovanni Palatucci, a Catholic, as a collaborator was at best hasty and more study was needed.
Palatucci had been previously credited with saving around 5,000 Jews while he was police official in the city of Fiume, now part of Croatia. He died in the Dachau concentration camp in Germany in 1945 at the age of 35.
But earlier last week, The New York Times reported that the US Holocaust Memorial Museum in Washington was removing mention of his exploits from an exhibition after officials learned of new evidence that purports to show he was a Nazi collaborator.
In her article in the Vatican newspaper, Foa, a Jewish-Italian author and historian at Rome's La Sapienza University, said the target of the move against Palatucci was "the Church of Pius XII".
"The impression is that ... in targeting Palatucci the desire was essentially to hit a Catholic involved in rescuing Jews ...," she wrote.
"But this is ideology and not history," she wrote.
The issue of whether the Vatican and the Church under Pius XII did all it could to help Jews had dogged Catholic-Jewish relations for decades. Pius reigned from 1939 to 1958.
Critics of Pius say he turned a blind eye to the Holocaust but his supporters say he worked behind the scenes to encourage the Church to save Jews because speaking out more forcefully would have worsened the situation for all.
Foa wrote that more documentation and study was necessary about Palatucci "from comparisons with other situations and not from interpretation."
The New York Times article said more than a dozen scholars from the Centro Primo Levi at the Center for Jewish History in New York reviewed nearly 700 documents before concluding that Palatucci was a Nazi collaborator and not a savior of Jews.
Among other things, the scholars concluded that Palatucci was sent to Dachau not because he helped Jews but because German occupiers accused him of embezzlement and treason.