Dai Yuming told reporters at a English-language press conference in Tel Aviv that the "errors to limit or even ban entries of Chinese citizens" reminded him of "the old days, the old stories that happened in World War Two, the Holocaust, the darkest days in human history."
"Millions of Jewish were killed, and many, many Jewish were refused when they tried to seek assistance from other countries. Only very, very few countries opened their door, and among them is China," Dai said.
The Chinese Embassy in Israel later issued a statement saying "there was no intention whatsoever to compare the dark days of the Holocaust with the current situation and the efforts taken by the Israeli government to protect its citizens."
"We would like to apologize if someone understood our message the wrong way," the embassy said.
Israel halted direct flights to China on Thursday, and Israel's Health Ministry has authorized border control agents to deny entry to non-Israelis who have visited China in the past two weeks. Israeli citizens who returned from China have been instructed to remain quarantined at home for two weeks in order to prevent the spread of the new coronavirus, which has killed more than 300 people and sickened thousands of others in China.
The number of coronavirus cases worldwide has passed 14,550, according to China's National Health Commission and other countries.
Most reported incidents are in China, but around 150 cases have been reported in two dozen countries around the globe.
Israeli Prime Minister Benjamin Netanyahu told ministers on Sunday that the country had "closed land crossings, seaports and airports to arrivals from China" for the time being. He said he has instructed the country's Health Ministry to develop a vaccine for the fast-spreading virus.
"We are also updating the Palestinian Authority on all preventive steps and public health measures that they must take into account here as well," he said.
The world marked the 75th anniversary of the liberation of the Auschwitz death camp last week.