The vaccine is proving only 9 percent effective in those 65 and older against the harsh strain of the flu that is predominant this season, the Centers for Disease Control and Prevention said Thursday.

Health officials are baffled as to why this is so. But the findings help explain why so many older people have been hospitalized with the flu this year.

Despite the findings, the CDC stood by its recommendation that everyone over 6 months get flu shots, the elderly included, because some protection is better than none, and because those who are vaccinated and still get sick may suffer less severe symptoms.

“Year in and year out, the vaccine is the best protection we have,” said CDC flu expert Dr. Joseph Bresee.

Overall, across the age groups studied, the vaccine’s effectiveness was found to be a moderate 56 percent, which means those who got a shot have a 56 percent lower chance of winding up at the doctor with the flu. That is somewhat worse than what has been seen in other years.

For those 65 and older, the vaccine was only 27 percent effective against the three strains it is designed to protect against, the worst level in about a decade. It did a particularly poor job against the tough strain that is causing more than three-quarters of the illnesses this year.

It is well known that flu vaccine tends to protect younger people better than older ones. Elderly people have weaker immune systems that don’t respond as well to flu shots, and they are more vulnerable to the illness and its complications, including pneumonia.

But health officials said they don’t know why this year’s vaccine did so poorly in that age group.

One theory, as yet unproven, is that older people’s immune systems were accustomed to strains from the last two years and had more trouble switching gears to handle this year’s different, harsh strain.

The preliminary data for senior citizens is less than definitive. It is based on fewer than 300 people scattered among five states.

But it will no doubt surprise many people that the effectiveness is that low, said Michael Osterholm, a University of Minnesota infectious-disease expert who has tried to draw attention to the need for a more effective flu vaccine.

Among infectious diseases, flu is considered one of the nation’s leading killers. On average, about 24,000 Americans die each flu season, according to the CDC.

This flu season started in early December, a month earlier than usual, and peaked by the end of year. Hospitalization rates for people 65 and older have been some of the highest in a decade, at 146 per 100,000 people.

Flu viruses tend to mutate more quickly than others, so a new vaccine is formulated each year to target the strains expected to be the major threats. CDC officials have said that in formulating this year’s vaccine, scientists accurately anticipated the strains that are circulating this season.

Because of the guesswork involved, scientists tend to set a lower bar for flu vaccine. While childhood vaccines against diseases like measles are expected to be 90 or 95 percent effective, a flu vaccine that’s 60 to 70 percent effective in the U.S. is considered pretty good. By that standard, this year’s vaccine is OK.

For senior citizens, a flu vaccine is considered pretty good if it’s in the 30 to 40 percent range, said Dr. Arnold Monto, a University of Michigan flu expert.

A high-dose version of the flu shot was recently made available for those 65 and older, but the new study was too small to show whether that has made a difference.

The CDC estimates are based on about 2,700 people who got sick in December and January. The researchers traced back to see who had gotten shots and who hadn’t. An earlier, smaller study put the vaccine’s overall effectiveness at 62 percent, but other factors that might have influenced that figure weren’t taken into account.

The CDC’s Bresee said there is a danger in providing preliminary results because it may result in people doubting — or skipping — flu shots. But the figures were released to warn older people who got shots that they may still get sick and shouldn’t ignore any serious flu-like symptoms, he said.