It's the first time flu shots will be available at about 600 pharmacies in Ontario.
The government cleared the way earlier this month for pharmacists to renew most prescriptions and offer some services previously provided only by doctors.
Matthews says she hopes allowing pharmacists to provide flu shots will bring the province's 33 per cent take-up rate closer to the 50 per cent level seen in some other provinces.
Pharmacies will be paid $7.50 for each flu shot given, and the government says new regulations allow pharmacists to add a charge for renewing prescriptions.
About 600 pharmacies are offering the shots against influenza this season.
The government expects all 3,500 pharmacies in Ontario will be able to offer the flu shots next year.