NHS hospital trusts in England may have to recalculate A&E performance figures from last October onwards.
The UK Statistics Authority has told NHS England to explain changes to the recording of A&E data.
It says the changes - highlighted by BBC News - could have left people reaching "misleading conclusions".
They raise questions over some trusts' performance on the highest profile NHS performance target - that patients in A&E are seen within four hours.
Dr Taj Hassan, president of the Royal College of Emergency Medicine, said: "The changes that are understood to have been made to recording practice throw doubt on whether the scale of the crisis facing emergency medicine - made so clear in December's data - is actually greater than first thought."
The letter focuses on advice given to trusts by the health regulator NHS Improvement.
Ed Humpherson, of the UKSA, says changes suggested by officials could "be having impact on recording practice."
The official target requires 95% of patients to be treated, assessed or discharged within four hours, a figure the NHS has failed to meet since July 2015.
A hospital trust's performance figures include the main accident and emergency department (known as Type 1) and minor injuries or care centres (known as Type 3).
These centres tend to see and treat patients a lot more quickly than those needing emergency care.
Data in these clinics tends to pull up the overall performance of a trust. This is confirmed by the Royal College of Emergency Medicine.
The BBC has seen emails sent by NHS Improvement, the body responsible for overseeing trusts, in October last year.
In one email titled "counting of A&E performance" sent to trusts in the south of England, it says they have committed to meeting the 95% target by March 2018 but that trusts had marginally failed to make the required progress.
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The email urged trusts to make sure they counted all their performance.
It said if "there is an urgent activity undertaken by a walk-in centre or urgent treatment centre or other provider within your local delivery board that currently is not reporting activity - we can work with you to apportion the activity to the main provider".
The implication is that including these centres would help improve overall performance.
This, and another email sent later in October by NHS Improvement, was seen by trusts as a request to add in data from walk-in centres not run by them and not on hospital grounds.
This is in direct conflict with clear guidance issued in November 2015 by NHS England, which says walk-in centre data can be included only if the trust has clinical responsibility for the service or if it co-located on the trust's grounds.
Analysis by the BBC shows as least six trusts in England have seen an improvement in their all A&E types four-hour performance figures in October compared with September by adding in walk-in centres not on their site and not run by the trusts.
It is thought some trusts have seen their four-hour performance improve by nearly much as 5%.
University Hospitals Coventry and Warwickshire NHS Trust A&E performance figures now include additional data for the City of Coventry Walk In Centre, which is run by Virgin Care Services and contracted by the local commissioning group
Another email from Jim Mackey, the outgoing chief executive of NHS Improvement, to trusts in October also wanted to make sure alternative pathways to A&E - such as urgent clinics - were included in trusts' performance data.
None of the changes is clear on the dataset produced by NHS England each month.
The data produced by NHS England for affected trusts is no longer directly comparable from October 2017 onwards with the corresponding months of preceding years.
An NHS Improvement official said it intended to address variation in the way A&E activity was being reported to ensure all trusts were reporting the same activity on the same basis.
"This change was not intended to artificially inflate A&E performance figures," the official said.
NHS Improvement denied any attempt had been made to secretly change the way figures were reported.
The Department of Health and Social Care said data should be collected as NHS England had suggested "so we have a clear and consistent picture of A&E performance across the country".
Figures for December 2017 show 85.1% of people were seen admitted, treated or discharged in England in all types of A&E department in four hours, the same as in January 2017, the worst performance on record.
The BBC understands Monday's intervention by the UK statistics Authority means the NHS will have to seriously consider reviewing and republishing data from October, when the NHS has been dealing with winter pressures.