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Two men, a 40-year-old man from Windsor and a 34-year-old man from Burnham were arrested on suspicion of producing cannabis.
A Legoland spokesman added the building was inaccessible to the public from the park and appeared to have been accessed from neighboring Crown Estate land owned by the Queen.
Both cannabis plants and equipment used to produce the drug were discovered in the building, which is being investigated by Thames Valley Police.
The two men arrested in the discovery were bailed until Feb. 28.