The pontiff responded after an Italian Jewish leader spoke of the painful "silence" of wartime Pope Pius XII.
It comes amid Jewish anger at Benedict's moves to beatify Pius.
The Pope conceded that "unfortunately, many remained indifferent", to the suffering of the Jews, six million of whom were killed in the Holocaust. But he said "The Apostolic See [the Vatican] itself provided assistance, often in a hidden and discreet way," without mentioning Pius XII by name.
His remarks came directly after the president of Rome's Jewish community, Riccardo Pacifici, told him "the silence of Pius XII before the Shoah [Holocaust], still hurts because something should have been done".
"Maybe it would not have stopped the death trains, but it would have sent a signal, a word of extreme comfort, of human solidarity, towards those brothers of ours transported to the ovens of Auschwitz," he said.
Some in the Jewish community, including at least one senior rabbi and a Holocaust survivor, boycotted the event.
The BBC's Duncan Kennedy in Rome says some Jewish leaders have called on the Vatican to open up its secret archives to study the record of Pius XII in closer detail.
That this issue is souring otherwise increasingly healthy relations between the two religions will frustrate many on both sides, but it is an issue that is unlikely to go away whilst Pius' path to sainthood is under consideration, our correspondent adds.
