Single shot immunisations given to toddlers at two private clinics - one in Sheffield and one in Hertfordshire - were not done properly, families have been told.
It means the children may not after all be inoculated against the childhood diseases of measles, mumps and rubella.
And the vaccines themselves may have become contaminated, leading to an increased risk of the children suffering bacterial infections.
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THE CLINICS INVOLVED
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Lifeline Care clinic at Hillsborough Sports Arena, Sheffield
Elstree Aero-Medical Centre in Hertfordshire, also run by Lifeline
Care
Jabs given between June and Dec last year
1013 children affected
All families involved have been sent letters
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Following controversy over suggested links between the three-in-one MMR injection offered by the NHS, and autism, the parents had paid the clinics for single injections of the vaccines instead.
The clinics are run by Lifeline Care Ltd.
At the clinic held at the Hillsborough Sports Arena in Sheffield, 718 children were given the faulty vaccines.
Another 295 were given the single dose vaccines at the Elstree Aero-Medical Centre in Hertfordshire.
The faulty vaccines were given at both clinics between June and December of last year.
The problem arose because the clinics changed the normal procedure for making up the vaccines, according to the local NHS trust in Hertfordshire.
'Not protected'
They began preparing batches of vaccines ahead of time, so more children could be treated - which investigators think may have led to the vaccines not working properly by the time they were administered.
The error only came to light after two doctors, who worked at the Elstree clinic, left and wrote a confidential letter to the local Hertsmere Primary Care Trust, which then investigated.
 We are recommending
parents get the children re-vaccinated with the MMR
Hertsmere Primary Care Trust
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Dr Joel Bonnet, director of public health at the trust, said, "As a result of the changes in the way the vaccines were made up there is a possibility that the efficacy of the vaccine has been affected, so that children are not as protected as normally they would be.
"There is a potential risk, which is why we are recommending parents get the children re-vaccinated with the MMR."
Dr Bonnet said he was unaware of any of the children who were not properly vaccinated, subsequently falling ill with measles, mumps or rubella.
The clinics concerned defended their actions.
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The vaccines were
used within the six-hour time scale recommended
Lifeline Care
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Dr David Pugh, medical director of Lifeline Care, told the Mail on Sunday they followed "common practice" when making up the vaccines.
"During last year we had particularly busy clinics and decided to reconstitute the vaccine in advance," he said.
"The vaccines were used within the six-hour time scale recommended. The view of the Department of Public Health was that the potency of the vaccine could not be guaranteed in those circumstances."
The clinics will be investigated by the National Care Standards Commission, which is the watchdog for all private medical clinics, and the General Medical Council.
The clinics have reverted to making up the vaccines as recommended by the manufacturer.
The Hertsmere Trust has written to all the families of the 1,013 children affected to tell them their children may not be properly protected.
It recommends that all children get the MMR vaccine.
Any parents who think their child might be affected can ring NHS Direct on 0845 4647.