The former federal Liberal leader was honoured for his tenure with a tree planted at the Corridor of Oaks garden at Faulconbridge in the NSW Blue Mountains on August 4.
The memorial contains oak trees planted by each of the nation's prime ministers, or their nearest surviving relatives.
But just days after Mr Abbott attended the ceremonial planting, a resident reported the tree had been destroyed.
The council plans to install CCTV at the site to deter vandals from striking again. (HANDOUT/MARK GREENHILL)
Blue Mountains City Council replaced the oak, only for its Labor mayor Mark Greenhill to learn that it had been vandalised again.
"I said 'no, no, that tree's been replaced' ... apparently it was gone again," Mr Greenhill told AAP on Tuesday.
A council crew which investigated on Monday night found the second tree had been ripped from the soil.
The garden was established in 1935 as a memorial for former NSW premier and "father of federation" Henry Parkes, who lived and was buried nearby.
Mr Greenhill said he was disappointed by the destruction as the trees honoured prime ministers of all political persuasions.
"It's a place that ... brings us all together to celebrate our democratic society," he said.
"It's not about the party ... it's about the tradition which is an important one for our local area."
The council plans to install CCTV at the site to deter further incidents.
Mr Abbott, who served as the nation's 28th prime minister before being deposed in favour of Malcolm Turnbull in 2015, said it was disappointing the tree had been vandalised.
But he welcomed the added security, noting in a statement that "a few of them have been damaged over the years by people unhappy with the PM who planted them".
Local Labor MP Susan Templeman also said she was disappointed to see vandalism at the Corridor of Oaks "no matter which side of politics is the target".
Council staff have alerted police and intend to increase on-site security.
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