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Two 26-year-old males and one aged 22 were located and apprehended by police dogs at the Glamis Hospital in Mornington at 10.40pm Friday night.
Senior Sergeant Craig Dinnissen said the men broke into the building and were damaging property.
They will appear in court tomorrow on a charge of unlawfully being on a property.
The building in Montpellier St has repeatedly been targeted by vandals, arsonists, trespassers and squatters since it was left vacant at least four years ago.
Neighbours have spoken about their frustrations of living near the site.
A representative told the Otago Daily Times in December owner Leng Seak Loke, who lives in Malaysia, planned to return Dunedin when he was able and make decisions about the building's future.