In two cases, reported by the Australian Jewish News, a five-year-old boy was allegedly called a "Jewish cockroach", while another Jewish student was made to kneel down and kiss the shoes of a Muslim classmate.
The parents of the five-year-old boy told the newspaper that their son wet himself in class after being bullied for four months.
Since hearing about the incidents, the treasurer has spoken to Victorian Premier Dan Andrews and Federal Education Minister Dan Tehan about the need to increase knowledge about the Holocaust.
"Billions of people lost their lives, including over one and a half million innocent children," he said.
"Everyone should know that story, it should be in our curriculums, it should be taught so we cannot repeat any of these mistakes of the past."
Parents pulling children from public schools
Victorian Education Minister James Merlino has ordered an "immediate review" of the handling of the alleged incidents and said he will meet with the parents who say the schools failed to address their concerns.
Anti-Defamation Commission chairman Dvir Abramovich has been in contact with the parents of the victims over the last three months and said it was the tip of the iceberg.
"Bullying and harassment of Jewish students at public schools is a deeply embedded menace that is reaching pitch-fever and should alarm us all."
"The kids are shaken and traumatised," Dr Abramovich said. "Too often, parents are concerned that the anti-Semitic abuse will escalate if they notify the school since their child will become even a bigger target.
He said some schools failed to acknowledge the incidents were driven by anti-Semitism and do not impose an appropriate punishment.
"Not surprisingly, there is mounting evidence that families are forced to take their children out and to enrol them in Jewish-day schools due to a growing sense of insecurity and fear that their kids will be harmed simply because of who they are."
Mr Frydenberg put a recent increase in anti-Semitic incidents down to intolerance and ignorance.
Such instances include swastikas across election material in Victoria and on a poster advertising a play about diarist Anne Frank, whose family took refuge from the Nazis in Amsterdam.
"That is just sickening, to say the least," he said.
The treasurer's Jewish mother was born in Hungary and fled to Australia to escape the Holocaust.