The first group of Australians fleeing the conflict crossed a land border out of Israel on Wednesday, assisted by the federal government.
Israeli ambassador Amir Maimon said he was personally involved in the Australian government's efforts to get people out.
"We are assisting the Australian government in every possible way," he told reporters on Thursday.
Israel's top diplomat in Australia said it was important to emphasise that the conflict with Iran was not about regime change.
"It is not for the State of Israel to decide about the nature of the regime in Iran, it is for the Iranian people," he said.
"We are focused on the military targets that were set."
For Australian mother-of-three Emily Gian, life in the days since Israel launched strikes on Iran and triggered waves of missile fire in retaliation has been spent in and out of underground bunkers.
"We could hear it so loud that my kids thought that it was near our house," Ms Gian told AAP on Wednesday.
"It's a really loud boom. You feel the house shake."
But unlike earlier conflicts with Hamas, Hezbollah and the Houthis, Ms Gian said the strikes from Iran came with the added fear that the nation was believed to be working on nuclear weapons.
"There's always been a fear in Israel that an escalation with Iran is the ultimate and scariest escalation that could be," she said.
But she won't flee.
"Our plans are to stay here for now because we live here, our house is here, our life is here, our work," Ms Gian said.
Melbourne lawyer Leon Zweir, who is in Jerusalem attending a conference, has registered with DFAT to be repatriated but will not leave until the event ends on Thursday.
He said the mood of Israelis was "resolute", despite the missiles flying overhead.
Amid concerns the US could enter the conflict, about 1200 Australians in Israel have registered with the Department of Foreign Affairs for help to leave, while 1500 Australians and family members have sought help to leave Iran.
Foreign Minister Penny Wong said a small group left Israel via a land crossing on Wednesday and that the department is looking for more ways to evacuate Australians.
"Obviously, the situation on the ground is fluid," she told ABC News on Thursday.
Evacuation was riskier in Iran, where the advice for Australians was to shelter in place if there was no opportunity to leave safely.
The conflict began on Friday after Israel moved to wipe out Iran's nuclear and ballistic missile program, claiming the Islamic Republic was on the verge of developing nuclear weapons.
US President Donald Trump has since met his national security council and demanded that Iran unconditionally surrender, adding he knew where Iran's supreme leader Ayatollah Ali Khamenei was hiding.
Iran has warned of "all-out war" if the US joins the fray.
Senator Wong said the Iranian regime threatened the stability of the Middle East.
"It's time, beyond time for Iran to come back to the negotiating table, for Iran to agree to discontinue any nuclear program," she said.
Israeli strikes on Iran have killed at least 639 people and wounded 1,329 others, according to Washington-based group Human Rights Activists, while Israel said at least 24 civilians had been killed.
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