Staff trying to migrate existing child immunisation records to new systems in London face a “complete mess”, according to a newspaper report.

The Department of Health has acknowledged the problems reported in the Sun, saying: “We know there is a problem with collecting surveillance data for the London PCTs. Senior officials at the Department of Health, Health Protection Agency and Connecting for Health are all looking at options for improving this situation.”

The newspaper ran an extensive account of difficulties being uncovered including an allegation that some children were recorded as having received nine vaccinations in a single day.

It reported that a leaked document entitled Summary of Data Quality Issues showed that up to 60% more jabs were recorded as having being given than would normally be expected.

The newspaper says that concerns about the state of the records have reached the highest levels with health minister, Caroline Flint, being briefed on the situation by Connecting for Health (CfH) chief executive, Richard Granger.

It quotes a source as saying: “It’s a complete mess. They don’t even know what they don’t know. Records for one borough are in such a poor state they could not be migrated on to the database. It looks like records for another 15 primary care trusts are just as bad.”

The source predicts existing records elsewhere in the country will be as bad as London’s.

Duplication of entries is seen as the likely explanation for some of the apparently high numbers of vaccinations given to children, but the newspaper suggests that some doctors may have inflated figures to hit targets for vaccinations.

The minister sent a letter to the newspaper saying she would take any allegations of fraud seriously but she ruled out the suggestion that over-ordering might be the source of fraud. “The system does not allow for this as doctors are paid for the immunisations they give irrespective of the number of doses they order,” she said.

“Ordering more vaccines would not improve their payments at all. However if the Sun, or anyone else, believes that doctors are deliberately giving more vaccines than children need just for the purposes of fraudulent claims then, of course, we would like to see the evidence for this.”

Childhood immunisation records became a source of friction earlier this year when clinicians in north-east London complained about the performance of the Child Health Interim Application (CHIA) devised by London local service provider, BT. Now the tables appear to have been turned with CfH raising serious questions about the child health service’s records.