A flight that left Lebanon on Thursday with 80 seats allocated for Australians had just 41 people take up the offer.
A further 500 seats are available on a flight that will leave Lebanon on Saturday, with only 238 Australians registering for the evacuation offer so far.
Assistant Foreign Minister Tim Watts said while Australians should get out of Lebanon on the evacuation flights, he admitted the decision to leave would not be easy for many.
"People have entrenched lives in that community, they live there, they have elderly family, they have businesses, they have properties, so it's understandable," he told ABC TV on Friday.
"This is a heart-wrenching decision to leave, but our advice is don't think twice about it."
Israel has intensified military action against Lebanon, bombing southern parts of the nation and its capital Beirut, which has killed hundreds of people.
Opposition Leader Peter Dutton also stressed Australians in Lebanon should leave at the first opportunity.
"If people are waiting for a RAAF flight, that is going to get more and more difficult. So I would just say that they should heed the advice of the prime minister: book that commercial flight now and get out of harm's way," he told reporters in Brisbane.
Israeli air strikes have hammered Lebanon, including the capital Beirut. (EPA PHOTO)
"There are commercial flights still available now as we pointed out before, there are still seats that are available. And people should take that up and leave straight away."
It comes as Israel has also threatened retaliation against Iran after it launched a missile strike.
Mr Watts said while Israel had the right to self defence, he pleaded for a de-escalation of tension in the region.
"We need to break this cycle of violence that we're seeing in the region. It's not in anyone's interest in the region to see a regional conflict, and that's really what we are on the brink of at the moment," he said.
Mr Dutton has also called for Iran's ambassador to Australia, Ahmad Sadeghi, to be expelled, following reports he praised Hezbollah leader Hassan Nasrallah as a "remarkable leader".
The Hezbollah leader was killed in Lebanon by Israeli air strikes.
"The comments from the Iranian ambassador are completely and utterly at odds with what is in our country's best interests," Mr Dutton said.,
"The prime minister and the foreign minister should show the strength of character and expel him from our country."
Organisers have agreed to change the location of a pro-Palestinian rally in Sydney on the weekend. (Jeremy Piper/AAP PHOTOS)
As a deal was struck to allow a protest to go ahead on Sunday ahead of the first anniversary of the October 7 attacks by Hamas, police forces from across Australia issued a joint statement calling for attendees to be peaceful.
"Police are lock-step in keeping Australians safe, and continue to work with all Australians, visitors, stakeholders, community leaders and leaders of faith to ensure Australian laws are understood," the statement said.
"Police are planning and preparing for upcoming protests in some states and territories."
Government Services Minister Bill Shorten said the protest should not be confrontational.
"Most Australians don't want to see these arguments from overseas coming to these shores. They certainly expect it to be peaceful," he told Nine's Today program.
"I'll just say to any protesters, if you think somehow you're convincing or changing anyone's mind, think again."
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