The missing fruit - which was taped to a wall to form the provocative work by Cattelan called Comedian - was noticed by a guard on Saturday to have gone missing.
The Pompidou-Metz museum, which is a branch of the famous Pompidou Centre in Paris, said in a statement it had lodged a criminal complaint for theft against persons unknown.
It also said it had replaced the banana.
It is not the first time damage has been dealt to the conceptual artwork, whose perishable banana centrepiece is replaced every three days to keep it contemporary.
In July last year, a visitor to the museum ate the fruit. But guards quickly intervened and stuck up a replacement banana.
Cattelan said at the time he was disappointed the hungry visitor had consumed only the banana and not the tape as well. The museum did not take legal action in that instance.
This time, though, it decided to make its criminal complaint because the perpetrator was unidentified, and therefore "there is no possibility of dialogue".
It also said that "this is the second time this has happened" and it felt it was an issue of respect for the artwork.
Cattelan's edible creation, which aims to question the notion of art and its value, has sparked controversy ever since it made its debut at the 2019 Art Basel show in Miami Beach with an asking price of $120,000.
A performance artist, David Datuna, ate Comedian at that 2019 show, saying he felt "hungry".
But the work's value has only risen.
Chinese-born crypto founder Justin Sun in 2024 forked out $5.2 million for one iteration of the work, then days later ate it in front of cameras in Hong Kong.
As well as "omedian, Cattelan is also known for producing an 18-carat, fully functioning gold toilet called "America" that was offered to Donald Trump during his first term in the White House.
A British court in March found two men guilty of stealing it during an exhibition in 2020 in the United Kingdom, from an 18th-century stately home that was the birthplace of wartime prime minister Winston Churchill.
It was split up into parts and none of the gold was ever recovered.
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