A group of about 30 protesters chanting, carrying placards and wearing 'They save We pay" t-shirts were waiting to greet Mr Luxon at the entrance to the Dunedin Public Art Gallery.
But Mr Luxon's motorcade stopped instead in Moray Place, at the back of the art gallery.
Mr Luxon was seen walking briskly past a smaller group of seven protesters.
The Prime Minister later exited the same way, greeted by a chanting group of protesters calling for a ceasefire in Palestine.
Last month, Health Minister Dr Shane Reti and Infrastructure Minister Chris Bishop made an announcement that the new Dunedin hospital would proceed in either a down-scaled version or by retrofitting the existing hospital. An estimated 35,000 people turned out in a protest that ended in the Octagon.
Health New Zealand Te Whatu Ora is looking to bring costs under control for the new hospital project’s inpatient building, after the government set a new budget of $1.88 billion. This did not include the pathology building or the carpark building.
Today's protest organiser Cr Steve Walker said the Prime Minister's decision to not enter through the front, past protesters, was "cowardly" on his part, but a win for the protesters.
"He's cognizant of the fact there is a voice in this city that he is unprepared to face up to and speak to and explain his side of the story ."
It was "completely inappropriate" for a Prime Minister to not face up to protesters - who just wanted answers to "fundamental questions".
"He is the man in the position, along with Dr Reti, who can give us those answers".
In the Octagon Noeline Speight, of Brockville, said the hospital was "very important" as it was a teaching hospital and was used by children.
The current hospital had leaking walls and was used to service the whole southern region.
It was "evil" what the government was doing to the city and Mr Luxon was not using his brain - "if he's got one to use," she said.
He was one of the estimated 35,000 people who turned up to the council-led protest in the Octagon.
The longer the government waited to build it, the more expensive it would be, he said.
With its chipped walls, the inside of the hospital was "like something out of the USSR".
"Just keep your promises."
Cr Walker has been leading calls for locals to make their feelings clear about government plans to shrink the new hospital.
"We need to make sure our voices are heard," he said in a Facebook post.