The foreign minister's visit to the region included meetings on Wednesday with officials from Israel and Palestine as calls for a ceasefire in the region grew.
Senator Wong said she would use Australia's position to call for the release of hostages taken during the October 7 attacks on Israel by Hamas.
After talks with Israeli President Isaac Herzog, Senator Wong met with the country's national security adviser Tzachi Hanegbi and visited a Holocaust remembrance centre.
She also visited the West Bank where she met with community members affected by settler violence since the Middle Eastern conflict escalated.
Senator Wong had previously shared "strong concerns the Australian people have about the death toll in Gaza" with the Israeli president.
In my meetings with — Senator Penny Wong (@SenatorWong) @Isaac_Herzog and @Israel_katz, I reaffirmed Australia's solidarity with the Israeli people following the atrocities of October 7. We unequivocally condemn the terrorist acts of Hamas and recognise Israel's right to defend itself, but how it does so matters. pic.twitter.com/XY1PGc9cQDJanuary 16, 2024
Her remarks were reinforced at home by cabinet colleague and Muslim MP Ed Husic, who told the ABC's 730 a more enduring and sustainable peace would come from Palestinians being able to have their own state.
"Too many innocent Palestinians have lost their lives ... and people should be able to speak up on behalf of humanity on either side, with respect to Israeli lives that were lost, but also the disproportionate number of Palestinians that have lost their lives," he said.
Senator Wong has also held meetings with Palestinian Prime Minister Mohammad Shtayyeh and Palestinian Foreign Minister Riyad al-Maliki.
It comes after Australia pledged $21.5 million in humanitarian aid for Gaza.
Chief executive of aid organisation World Vision Daniel Wordsworth said while the funding was welcome, the desired outcome was a ceasefire.
"A sustainable ceasefire is critical but so is a long-term, peaceful solution for children in the region," he said.
"Not only are we seeing children killed in Gaza, but we're also seeing children face a lack of access to the humanitarian aid they need to survive."
The federal government has also come under fire for not supporting a case in the International Court of Justice, where South Africa has accused Israel of committing genocide against Palestinians in Gaza.
Senator Wong said while Australia respected the independence of the court, it did not mean it supported the premise of South Africa's case.
"We will continue to work for a just and enduring peace between Israelis and Palestinians," she said.
Prime Minister Anthony Albanese noted Australia was not a participant in the case against Israel but said "that doesn't mean we agree with some of the assumptions they have in the South African case at all".
Senator Wong will also travel to the United Arab Emirates as part of her week-long visit to the Middle East.
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