The HPA said the figures showed there was "room for improvement" in testing people in at-risk groups.
At risk groups include the over-65s, pregnant women, people with weakened immune systems and other health conditions.
Currently it is estimated that only around half of those at risk groups are taking up the vaccine.
Other life insurers, who consider the company to be a leader in insuring high-risk groups, are watching carefully.
Focused screening and information for high-risk groups could end the epidemic, experts say.
He said anyone in at-risk groups such as that should seek vaccination which he described as "safe and effective".
Profits from the event, in its 31st year, will aid young people, at-risk groups and people with special needs.
We would need more evidence that more than these six key, target high-risk groups that are prioritized can benefit.
It would then be offered to high risk groups across the island who already receive the seasonal flu vaccine.
The report is vague about funding and needs to be more specific about who the 'high risk groups' are.
Infants and their siblings, parents and caregivers are now also supposed to get the vaccine in addition to traditional high-risk groups.
Since 1992 its small but dedicated staff has been testing high-and low-risk groups in 19 places in the country twice a year.
Their six-gene test could split patients into high and low risk groups.
The Chief Medical Officer Dr Ruth Hussey said she wanted to encourage as many people as possible in high risk groups to get vaccinated.
BBC: Flu jab given at some pharmacies in Wales for first time
Children in at-risk groups, such as those with asthma, heart conditions or cerebral palsy, are already eligible to receive the vaccine from their GP.
It is reached when heat is so severe that illness and death may occur among the fit and healthy, and not just in high-risk groups.
But even among these high-risk groups, the vaccine can prevent complications.
He said early evidence had suggested up-take was not higher than previous years and there should have been enough doses for all the at risk groups.
At most, the study suggests that people in high risk groups who know they are likely to get a genetic disease can handle negative health information.
Work on the front line of the epidemic among the high risk groups such as addicts and prostitutes is left to organisations like the Alliance, he says.
Flu is generally just means taking time off work for most people but certain at-risk groups are prone to developing potentially fatal complications, such as bronchitis and pneumonia.
"In the meantime, for the forthcoming flu season, our priority remains to ensure a high uptake rate is achieved in the at risk groups including pregnant women, " he added.
Secretary of State Hillary Clinton stressed the importance of reaching high-risk groups, including female sex workers, on July 23 in her remarks at the bi-annual International AIDS Conference.
The DoH has therefore launched a campaign to encourage at-risk groups to get vaccinated and a new website, called Winterwatch, will be launched later this month to provide winter-related health data.
He said current guidelines which say TB patients should only be offered testing - along with counselling and informed consent - if they are from high-risk groups or areas should be reviewed.
The RNIB is urging people in high risk groups to have regular eye tests to pick up the onset of the condition and, if it is diagnosed, to adhere to medical advice.
"The overall long-term goal is to use these findings to develop faster and better means of identifying early atherosclerosis in high risk groups and prevent its progression to full blown heart disease, " he said.
Studies like the one one on chlamydia and gonorrhea will hopefully help flesh out the interaction between internet hook-ups and health risks so that we can better target at risk groups for preventative education.
She has decided against vaccinating herself and her 12-year-old son both because she doesn't believe there is enough safety information about it, and because she doesn't think she and her son are in high-risk groups.
The rate at which an epidemic spreads to lower-risk groups depends a great deal on whether different groups mate mainly among themselves (assortative mating) or whether they mate a lot with other people (disassortative mating).
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