Child vaccination rates may be falling to risky levels after a new IT system was installed, a health watchdog says.
Child vaccination coverage has fallen in some areas
Ten out of London's 31 primary care trusts have installed new software to manage the vaccine programme as part of a £6.8bn overhaul of NHS computers.
Only two have been able to provide data on MMR and the five-in-one jab uptake and these show drops of up to 19%.
The Health Protection Agency said it was investigating.
It also means information is missing on over 50,000 children, which can also potentially put them at risk.
Without proper data, doctors cannot make appointments and send out reminders when children are due follow-up jabs.
It is the latest in a long-line of controversies to dog the upgrade of the health service network being administered by a government agency called NHS Connecting for Health.
The 10-year programme has only been running for two years and is aimed at linking more than 30,000 GPs to 300 hospitals, but has already been criticised for the high cost and being behind schedule.
As part of the upgrade, a new system to administer the vaccination programme was installed in parts of London.
Only two PCTs - Barking and Dagenham, and Havering - have been able to supply data for the past year.
The information shows a fall in MMR vaccine rates by up to 10% and the five-in-one jab, which protects from diphtheria, tetanus, whooping cough, polio and Hib disease, by up to 19% in the past year.
The HPA warned falls of this magnitude "not only indicate individual children may be at risk, but also represent a major public health threat".
HPA immunisation expert Natasha Crowcroft said it was being investigated.
"It is by no means certain whether they are true falls in coverage over the last year or if indeed, they just reflect data quality problems relating to the implementation of the new child health systems."
Richard Bacon, a Tory MP and member of the Commons' Public Accounts Committee, said: "The national vaccination programme has been one of the NHS's greatest successes."
But he added the IT upgrade appeared to be "destroying it at a touch of a button".
Liberal Democrat health spokesman Steve Webb described it as "shambolic".
"We are not talking about the latest software for SimCity - real lives are at risk if we get this wrong."
A spokesman for NHS Connecting for Health said the new system was implemented at short notice because the previous supplier "withdrew support for its ageing system from the market".
"We acknowledge there have been issues with the new computer system which we regret. The alternative of no computer system would have been far worse."