The median rate of scanning was just 10 per cent and at 12 venues, eight of which were bars, no-one scanned in at all during the survey period.
One cafe had 44 patrons, only one of whom scanned in.
At 10 bars, from a total of 184 customers, just four scanned in.
Supermarket customers were slightly better, recording scanning rates between 11 per cent and 30 per cent.
At one church service a quarter of attendees scanned in, but at another none of 57 worshippers present scanned in on arrival.
"Beliefs that Dunedin is somehow safe from Covid-19 are worrying as they ignore the mobile nature of the population in New Zealand," Associate Prof Lianne Parkin said.
"For example, University of Otago students from Auckland were permitted to travel to Dunedin while Auckland was still at Alert Level 3 and thousands of students from all over the country recently arrived in Dunedin in time for the large social events associated with Orientation Week."
Researchers randomly selected 10 cafes, 10 restaurants, 10 bars, five churches and five supermarkets, and observed scanning behaviour over an hour during peak times.
Most venues were surveyed from January 24-27, just after community cases of Covid-19 were detected in Northland and Auckland — a scare which resulted in the total number of scans at a national level increasing markedly.
"It is impossible to know whether the low proportions we observed in Dunedin during the same period were actually an improvement on previous proportions, or conversely whether there was no change in scanning proportions because people perceived that the local risk associated with the North Island cases was very low," Prof Parkin said.
Researchers also looked at whether QR code posters were displayed correctly.
They found that at seven venues the code was not correctly printed on A4 paper or had been cropped, at four the code was not displayed prominently near the main entrance, and at two high glare on the poster meant it could not be properly scanned.
