Ideally, children would be vaccinated before school starts, but the H1N1 vaccine won't be available until mid-October, making schools a logical place for mass vaccination, Duncan told CNN's "American Morning."
"It will be a two-shot sequence," Duncan said. "And so we want to be very thorough on this and make sure as many children who want to get vaccinated have an opportunity to do that right in their schools."
So far this year, more than 1 million U.S. residents have been infected with the H1N1 virus with 353 deaths reported, especially among young people and those with damaged immune systems.
Parents should teach their children the importance of coughing into their sleeves and washing their hands frequently, Duncan said,
"We have to prepare for the worst," Duncan said. "The honest answer is we don't know how bad this will be."
CDC: Get your flu vaccine