Asked to comment on Netanyahu's allegation, government spokesman Steffen Seibert said he would not speak directly on the claim.
But he added: "I can speak for the federal government, that we Germans recognise that the murderous racial fanaticism of the Nazis was the historical origin of ... The Shoah.
"I see no reason to change our view of history in any way. We know of the inherent German responsibility in these crimes against humanity," he added, just hours before Netanyahu was to meet German Chancellor Angela Merkel in Berlin.
"Hitler didn't want to exterminate the Jews at the time. He wanted to expel the Jews," Netanyahu told the World Zionist Congress.
"And Haj Amin al-Husseini went to Hitler and said: 'If you expel them, they'll all come here.' 'So what should I do with them?' he asked. He said: 'Burn them.'"
Netanyahu today backtracked on the claim, denying that he was exonerating Hitler of the responsiblity for the Holocaust, in which six million Jews were slaughtered.