Young infants may get an extra dose of meningitis C vaccine to boost their protection against the potentially fatal disease.
Meningitis produces a characteristic rash
Some infants immunised when they were younger than five months did not have long-term protection, the Health Protection Agency has found.
It says government should consider changing the current immunisation schedule.
The Department of Health said it was seeking further advice.
The UK introduced the meningitis C vaccination into the routine childhood immunisation schedule in November 1999.
This was because meningitis C had infected about 1,530 people and caused 150 deaths in 1998, mainly in children and young adults.
Under the schedule, a dose of the meningitis C vaccine was given to infants at two, three and four months of age.
The vaccine was also offered to all children younger than 18 years in a catch-up campaign designed to quash rates of infection.
In 2001, there was a 90% reduction in cases and deaths from meningitis C.
In 2002, the government extended the programme to include people younger than 24.
Dr Mary Ramsay and colleagues at the HPA looked at surveillance data for the last four years since the introduction of the vaccine programme.
The vaccine offered high levels of protection in the first year, regardless of the age of the child at the time they were immunised.
Thereafter, the vaccine remained highly effective in children aged five months to 18 years, protecting nearly 90% of those immunised.
But it's protection waned in children younger than five months.
Only two-thirds had immunity against meningitis C a year after they had been vaccinated.
The researchers identified 53 vaccine failures overall, 21(40%) of which were in children who had been routinely immunised as an infant.
The researchers said this rapid waning was worrying.
Despite this, they said few infants were catching meningitis, probably because the rest of the society had been successfully immunised.
They said their findings reflected what was happening with immunity conferred by the childhood Hib (haemophilus influenza type b) vaccine, which is given at the same stages in infancy.
They believe the critical factor for both meningitis C and the Hib vaccines is the age at which the final dose is given.
Change in policy
Dr Ramsay said: "Alternative vaccination schedules must be seriously considered
"One way is to put a booster in at maybe the second year of life or later.
"The other way would be to change the schedule to spread it out over a longer time.
"Maybe you could get away with two doses early in life and one later, say two, four and six months or two, four and nine months for example."
She said they would study these options and continue to monitor immunity levels in older children.
Dr George Kassianos, a GP in Berkshire and immunisation spokesman for the Royal College of General Practitioners, said it was "extremely reasonable and desirable" to suggest booster doses might be needed.
He said the best time to give children an extra dose would be when they visited their GP for their MMR vaccine.
A spokeswoman from the Department of Health said: "It's a very interesting study commission to look at the long term effects and we will now be referring it to the Joint Committee on Vaccination and Immunisation and the Committee on Safety of Medicines for further advice."