He will appear in the Dunedin District Court on a "number of charges", police said.
A second Milton man known to police is being sought.
The property is owned by Davis Shearing Contractors Limited.Owner Jayson Davis said he could not comment on the incident because police were still investigating.
"I'm not at liberty to give any statements at the moment, still waiting to hear back from the report. That's as far as it goes really," he said.
He said he understood police were still conducting enquiries at the Arthur St site.
Southern Police Senior Sergeant Craig Brown said officers were following a "positive line of enquiry".
He said he could not release any more information at the moment but further details should be available this afternoon.
A shearing quarters on Arthur St hit headlines last year when escaped prisoner Stephen Uriah Maddren was found sleeping in its hot water cupboard.
It is understood to be the same property where the alleged assault took place last night.
Police recaptured Maddren - who was the only person to have escaped from the Otago Corrections Facility at Milburn - in June, 2014.
Maddren was discovered asleep in the rural property's hot water cupboard after being on the run for a week.
It is thought he escaped barefoot by climbing a downpipe onto a prison roof and jumping from a height of two or three storeys.