The comments come less than a week after Turkey appointed a foreign policy advisor to the prime minister as ambassador to Israel, sealing the normalisation of diplomatic relations after a six-year partial rupture.
"I don't approve of what Hitler did, and neither do I approve of what Israel has done. When it's a question of so many people dying, it's inappropriate to ask who was the more barbarous," Erdogan said in an interview with Israeli television on Monday night.
The relationship between the two countries plunged to an all time low after an Israeli commando raid on a Gaza-bound ship in 2010 that killed 10 Turks, prompting Ankara to expel the Israeli ambassador and freeze all defence ties.
But the two sides have been working to bring cooperation back to former levels and are holding talks on building an ambitious pipeline project to pump Israeli gas to Turkey and Europe.
Nevertheless, considerable tensions remain with Erdogan presenting himself as a champion of the Palestinians and regularly meeting with Hamas chief Khaled Meshaal.
Israel, the United States and the European Union all view Hamas, which governs the Gaza Strip, as a terrorist organisation.
It is not the first time that Erdogan has referred to the World War II Nazi leader when dealing with Israel.
After the 2010 raid, he accused Israel of "keeping Hitler's spirit alive".
And during the 2014 Gaza War, in which 2,251 Palestinians were killed, according to the UN, he said Israelis "have no conscience, no honour, no pride. They curse Hitler day and night, but they have surpassed Hitler in barbarism".
He has accused the Jewish state of carrying out "genocide" on the Palestinians.
In Monday's comments to Israel's Channel 2 television, Erdogan said he was "well aware" of the sensitivities associated with Hitler, blamed for the deaths of some six million Jews.
But he said he found it "impossible to forget the hundreds, the thousands of people who died when (the Israeli military) struck Gaza".