Their absence could embarrass Japanese Prime Minister Fumio Kishida, set to attend the annual event, which typically draws less attention than one held in Hiroshima three days earlier to mark the first-ever use of nuclear weapons.
"It's not that we haven't issued an invitation to the Israeli ambassador for political reasons, but rather, we want to conduct the ceremony smoothly in a calm and solemn atmosphere," said Nagasaki's mayor, Shiro Suzuki.
"There has been no change in that judgment," he added, but did not elaborate.
The exclusion puts Israel on a list of uninvited countries that includes Russia and Belarus, although its ambassador, Gilad Cohen, attended this year's ceremony in Hiroshima.
The Nagasaki mayor's snub comes as Israel continues to fight Hamas forces in Gaza, a conflict that has reduced much of the heavily populated strip to ruins and killed more than 39,600 Palestinians, according to Gaza health ministry figures that do not distinguish between combatants and civilians.
"Russia's invasion of Ukraine and Israel's self-defense are not morally equivalent," U.S. Ambassador Rahm Emanuel said, in a comment provided by the embassy in Tokyo.
"Unfortunately, because of the mayor’s decision, the message of that ceremony and memorial will be distracted and deflected."
Japan's chief government spokesperson, Yoshimasa Hayashi, declined to comment when asked about the matter at a regular press briefing on Thursday.
Israel's embassy in Tokyo did not immediately respond to a request for comment.
Last month, Emanuel and other G7 ambassadors, including those of Britain, Canada, France, Germany and Italy, along with the European Union representative, sent a letter to Suzuki expressing concern at Israel's exclusion.
The grouping of major democracies has urged restraint and de-escalation in the Middle East amid heightened tension, but stays committed to supporting Israel.
Eight decades after the atomic bombings precipitated Japan's surrender to end World War Two, the anniversaries in Nagasaki and Hiroshima, which is Kishida's hometown, still evoke strong feelings in Japan.
Although the exact number of casualties is unknown, the atom bombs dropped by the U.S. are estimated to have killed more than 200,000 people.
