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.