The apology followed a complaint by the Japanese ambassador to Israel, Hideo Sato, after senior government official Daniel Seaman disparaged commemorations for the victims of the 1945 atomic bombs, causing a wave of protests in Japan.
"I am sick of the Japanese, 'Human Rights' and 'Peace' groups the world over holding their annual self-righteous commemorations for the Hiroshima and Nagasaki victims," Seaman wrote on his Facebook page. "Hiroshima and Nagasaki were the consequence of Japanese aggression. You reap what you sow."
According to the Haaretz newspaper, Israel's ambassador in Tokyo, Nissim Ben-Shitrit, was forced to embark on a damage control exercise. "The incident is very slowly subsiding, but it's too early to assess the damage to Israel's image that it caused," the Israeli embassy in Tokyo wrote in a cable to the foreign ministry in Jerusalem.
The apology was issued by Ya'akov Amidror, national security adviser to the Israeli prime minister, Binyamin Netanyahu. A government official said the incident was "one of the least comfortable moments for Israel in Japan".
Seaman, a former director of the government press office who has a reputation for being abrasive, recently took up a new post to promote positive images of Israel on social media networks. He has since been suspended and is under orders not to speak to the media.
The comments about Japan were part of a string of strongly worded postings by Seaman over recent months.
They included a response to a demand by the Palestinian chief negotiator, Saeb Erekat, for an end to new settlement expansion that read: "Is there a diplomatic way of saying 'Go F*** yourself'?"
At the start of Ramadan, Seaman posted: "Does the commencement of the fast of the Ramadan means [sic] that Muslims will stop eating each other during the daytime?"
In response to a Church of Scotland report that argued that Jews do not have a divine right to the land, he wrote: "Why do they think we give a flying F*** what you have to say?"
In a statement last week, Israel's National Information Directorate said: "Danny Seaman's statements on Facebook are unacceptable and do not express the view of the Israeli government. The directorate instructed Seaman to immediately refrain from making such statements."