A man has been "seriously injured" during an incident at the Dunedin Courthouse.

Duty lawyer Max Winders said two men were involved in the alleged assault in the cells this morning. The victim was taken to Dunedin Hospital.

Both were serving prisoners at the Otago Corrections Facility and were due to appear today, along with another man, before the Dunedin District Court on a charge of injuring with intent to do grievous bodily harm, from an alleged incident at the prison on April 1.

Ambulance officers were seen just before 9.30am carrying a stretcher into the cell entrance to the courthouse on Castle St.

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About 10 minutes later, a young man who appeared to be unconscious was carried into the ambulance on a stretcher with his head in a brace.

He appeared to be of Maori or Pacific Island descent.

St John spokesman Gerard Campbell later confirmed a man with serious injuries had been transported from the court this morning.

A Corrections Officer escorted the injured man to Dunedin Hospital.

Earlier, people could be heard banging on the internal walls of the police custody van as it drove towards the building.

Police prosecutor Sergeant Mike Wingfield said CIB wanted to interview the two men involved in the alleged assault with a view to further charges being laid.

In court, Winders suggested all three should be remanded until Tuesday without appearing. Police supported that stance.

Judge John Macdonald said if there was a security risk posed by the defendants, it would be "classic case" for them to be called by audio-visual link, rather than brought to court again.