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Sir Elton landed at Dunedin Airport on a private jet from Sydney about 2.45pm.
The plane was inspected by Customs and MPI before he left with a small entourage and was taken away in a private vehicle.
Meanwhile, fans of Sir Elton visiting Dunedin have been greeted with wet weather and some of the heaviest rain is expected to fall in the hours leading-up to tonight's concert.
A heavy rain warning is in place for Dunedin from 9am to 10pm today during which 40mm to 70mm of rain is expected to accumulate.
Gates open at Forsyth Barr Stadium at 5pm and opening act Tate Sheridan is expected on stage at 6.30pm.
The forecast has eased a little and now 6.5mm of rain is expected in Dunedin between 4pm and 6pm, 8mm between 6pm and 8pm and 13.2mm between 8pm and 10pm.
Forsyth Barr Stadium does not typically allow umbrellas inside, but due to the forecast rain is allowing them to be stored at the gates on arrival.
"They will be labelled and kept at the gates for collection as fans leave."
Some fans may struggle to make it after many roads across the South were closed due to flooding.
Emergency Management Otago acting director Michele Poole encouraged those travelling into Dunedin to be safe and careful while driving and to adhere to road closures and warnings.