South Australia is in the grips of an "unprecedented" flu season with 17 deaths and more than 12,300 confirmed case so far this year.

SA Health says the 12,339 cases in 2019 compares to 1348 at the same time last year, but remains the "tip of the iceberg" in terms of the number of cases in the community.

"This is an unprecedented year. We have never seen influenza in these numbers at this time of the year," Chief Medical Officer Paddy Phillips told reporters on Monday.

"We know that the reported cases is the tip of the iceberg.

"Influenza is unfortunately everywhere in our community.

"It's in supermarkets, it's in workplaces, it's in schools, it's in sporting clubs and it's in nursing homes."

Of the 17 deaths, all but one, a 15-year-old, were aged above 60.

Thirteen of the deaths occurred in residential aged care facilities with five in one centre alone.

Since January there have been 53 reports of flu outbreaks at nursing homes in SA with the number of flu-like cases reported in each home between three and 40.

Professor Phillips said there had also been unprecedented demand for doses of the flu vaccine with about 456,000 delivered so far.

He said only time would tell if the high number of cases would continue through winter.

However, he was hopeful the early spike and the high take-up of the vaccine would result in the numbers tapering off.