How much protection the influenza vaccine provides overall varies every year. Over the past 10 years, at best it was 60 percent effective and at worst about 20 percent effective, according to CDC data.
The CDC measures effectiveness as whether the vaccine prevents illness and patients from seeing a doctor. For Thursday's report, the agency analyzed cases of 4,562 children and adults with flu-like symptoms who visited one of the five U.S. Influenza Vaccine Effectiveness Network sites.
In a statement, Food and Drug Administration Commissioner Scott Gottlieb said although the vaccination effectiveness is "better than some might have predicted, there is still clearly significant room for improvement."
"The FDA is committed to working together with the scientific and medical communities to better protect the public against the flu and apply lessons learned to next season's flu vaccines," Gottlieb said.
The FDA meets every February to choose what to put into the year's flu shot based on recommendations from the World Health Organization. They include three or four strains, since multiple viral strains can circulate throughout the season.
The FDA may pick a good match, but the influenza virus often mutates, sometimes so much that the vaccine elicits immune responses that do not recognize it and therefore struggle to fight it. There aren't any signs that phenomenon occurred this year, the CDC's Schuchat said Thursday.
Another problem scientists have identified is the virus mutating while developing in eggs.
"That's an issue we're looking at very intensely across (the Department of Health and Human Services) and with the private sector to understand whether there are better ways to ensure that we're producing effective vaccines," Schuchat said.
Some companies have already started producing vaccines in cells. Seqirus, the vaccine unit of Australian manufacturer CSL, produced cell-based flu vaccines at commercial scale at one of its facilities last year in what the company called an industry first.
Sanofi Pasteur last year acquired Protein Science, which makes Flublok, an influenza vaccine manufactured in insect cells. Now that Sanofi Pasteur has the product, the company will see if it can apply the process more broadly, John Shiver, global head of research and development, told CNBC last month.
Scientists' ultimate goal is to create a universal flu vaccine that could be administered once and prevent sickness for a lifetime. Achieving that is likely still far off. So in the meantime, the current shots are people's best options for preventing the flu.
The CDC says it's not too late to get a shot. It expects the flu season to last several more weeks, and some protection is better than none.