The mismatch is occuring among the A-strains of the flu vaccine. All flu shots contains a combination of A and B-strain viruses that vary each year, depending on which bugs scientists believe are most likely to cause illness.
The Minnesota Department of Health says up until the beginning of February, more than 93 percent of the state's flu cases were well-matched to the vaccine -- compared with just 50 percent nationally.
But immunizations manager Kris Ehresmann says since then, the virus circulating in Minnesota has changed.
"We thought it was important that people know that we, too, are starting to see some of the trend that has been happening nationally," says Ehresmann.
Ehresmann says people who get the flu shot still have more protection than those who don't get vaccinated.