Isaac Herzog planned to begin the last day of his four-day Australian tour at the site of Melbourne's Adass Israel synagogue on Thursday morning.
The Ripponlea temple has been closed since it was firebombed in late 2024 but remains a site of deep significance to the local Jewish community.
However, Mr Herzog's visit to the site was cancelled amid security concerns in a development that left members of the congregation feeling "very uncomfortable," Adass member Abe Weiszberger told AAP.
"To call it a shame would be an understatement," he said, reflecting on the significance of the visit for the grieving Jewish community.
"When someone comes here to comfort you and they come to be with you in your home, what do you think that feels like?"
Mr Herzog was invited to Australia by the federal government in the wake of the Bondi terror attack.
Concerns about Israel's actions in Gaza, however, have contributed to a hostile reception from protesters and some politicians.
At least nine people were charged, and 27 arrested after protesters were punched and pushed by police when an anti-Herzog rally turned violent in Sydney's CBD on Monday.
More than 5000 people are expected to protest at Flinders Street Station on Thursday evening in opposition to Mr Herzog's invitation.
While Victoria Police said there was no specific threat to the president, they were given special powers under terrorism legislation ahead of his visit.
Daniel Aghion, president of the Executive Council of Australian Jewry, is travelling alongside Mr Herzog through Melbourne on Thursday.
Asked what he made of the planned protests, Mr Aghion urged Victorians to remember the reasons behind the president's visit.
"Those who are protesting his visit should think about what the Australian Jewish community has suffered and whether it is appropriate for protest about an international conflict to be made at this time," he told AAP.
Mr Weiszberger said he was more concerned about the days and weeks after Mr Herzog's visit, when police would be stripped of their powers.
"I think the concern is more going forward," he said.
The federal government pledged $31 million towards rebuilding the Adass Israel synagogue last year, ahead of an expected 2029 reopening.
