The present Croque-O-Dile Cafe lessee David Law said his lease on the building was not going to be renewed after June 10.
The cafe would operate until then and then close temporarily.
He said the Dunedin City Council would take time to complete some overdue maintenance before finding a new lessee.
He said he originally had a lease until August this year for the premises but the cafe’s manager Kristine Lind’s ill health meant they had to leave earlier.
The Dunedin Botanic Garden said it was investigating alternative food and beverage options while the cafe was closed.
"We acknowledge the cafe is a much-loved institution within our wonderful garden and reassure our many visitors that we remain committed to having an awesome cafe at this location."
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