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Prison manager Jack Harrison confirmed an officer was taken to Dunedin Hospital for assessment following the early morning incident at the Milburn prison.
No weapon was involved, Mr Harrison said.
The Otago Daily Times understands the officer was knocked out during the altercation.
A Corrections Department spokesman said the guard went home from hospital yesterday and was off work recovering.
The department was unable to confirm the nature of the incident, or the identity of the prisoner.
Two other officers were taken to Dunedin for medical treatment, before being sent home.
The prisoner had been relocated to a management unit and his security classification was being reviewed.
Police were investigating the incident.
Mr Harrison said any assault on a staff member was ''extremely concerning''.
Serious prisoner-on-staff assaults at the prison were rare, he said.
Before yesterday's incident, there had been nine assaults on prison staff by inmates since July 2013.
Seven assaults had resulted in non-serious injuries and two had caused no injuries.
Corrections had a zero tolerance policy towards prisoner assaults on staff and other prisoners.
To reduce assaults in 2013-14, the prison was introducing anti-violence campaigns and a pilot prison risk assessment tool to identify issues in prisons contributing to prisoner violence