Emergency services were called to the court just before noon.
The man appeared to have suffered self-inflicted wounds, a police spokeswoman said.
"It's not clear whether he was appearing in court or whether he was there for another reason,'' she said.
"An ambulance was called but hasn't arrived yet, so police took him [to Dunedin Hospital] themselves.''
The extent of his injuries are unclear, but police cars and an ambulance were visible outside the courthouse a short time ago and it appeared the pavement was being washed down.
Court staff appeared to be cleaning outside. It is understood the injuries were inflicted in a bathroom inside the court house.
Where to get help:
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- Youthline: 0800 376 633
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- Rainbow Youth: (09) 376 4155
If it is an emergency and you feel like you or someone else is at risk, call 111.