Some schools are registering absentee figures of about 20% - twice the national winter average for New Zealand schools - and a South Dunedin health clinic believes the after-effects of June's floods could be a factor.
While schools on the flat - the area most affected by June's flooding - were recording surging absentee numbers, schools from other parts of Dunedin were showing significantly different results.
Not one of the schools contacted by the ODT from areas other than southern Dunedin had absentee rates higher than 10%.
In contrast, not one school on ''the flat'' had an absentee rate lower than 10%.
The Ministry of Education's most recent records (2013 school year) show average winter absentee rates across the country were 10%.
Aurora Health Centre practice manager Sharon Smith said the South Dunedin clinic had noticed a ''huge increase'' in patients with flu-like illnesses over the past few weeks.
''There are heaps and heaps of them coming in every day. It does feel particularly bad this year.''
She said it was possible the after-effects of June's floods were a factor, citing both the possibility of damp housing and the stress for those who had needed to relocate, have belongings thrown out and replaced, and deal with insurance companies.
''For a lot of our people, the last few months have been pretty full on.''
And the illness spared no-one once it took root in a family, Mrs Smith said.
If one member of a family came in with flu-like symptoms, other family members inevitably followed days later.
She said the illness seemed to be affecting all ages.
Mornington Health Centre practice manager Jo Rowe said there had been a noticeable spike in the number of patients with flu-like symptoms at her clinic in the past couple of weeks.
The common cause appeared to be viral upper respiratory tract infections, she said, causing raised temperatures, breathing issues, coughing and sore throats.
King's High School, which had seen absentee rates soar to 23% this week, was asking pupils and their parents to use common sense if they were ill, rector Dan Reddiex said.
''We're assuming they're going to apply common sense along with their parents - they're the ones best informed to make those choices about whether they should or shouldn't go to school,'' Mr Reddiex said.
It was not the first time the school had been hit hard by illness in recent years, but ''certainly, a large proportion of students have been hit hard this time around''.
He said this illness tended to leave pupils off sick for multiple days, ''rather than just singles''.
St Clair School principal Richard Newton said while a winter spike in illnesses was expected every year or two, ''I think this little bulge is in advance of the norm''.
Symptoms at his school tended to begin with general unwellness, headaches, lethargy and muscle aches, before progressing into cold symptoms - runny nose, itchy red eyes, and coughing.
He said it was the cough that was lingering - for some it was lasting several weeks.
The flu-like flare-up follows late June's outbreak on the Taieri, where on one particular day 100 of East Taieri School's 310 pupils were absent, along with five staff.
