Duplicate employment records from payroll ID changes

Q: Why does a changed payroll ID create a second employment?

HMRC's own examples show three ways it goes wrong: Change in month 1 without the old ID. Only one FPS is held for the new year, so there is no earlier year to date figure to test against. The match fails and a duplicate is created from month 1. Change mid year with a keying error. The old ID is omitted and the carried forward year to date pay has two digits transposed. The arithmetic test fails and a duplicate starts from that month. Reusing an old ID for a returning employee. This is the opposite problem. Two separate periods of employment are merged, so HMRC ends up with one end of year record based on the last FPS and ignores the earlier pay. HMRC's compliance guidelines GfC22 list the usual triggers for an ID change: changing payroll software, changing payroll provider, a restructure, or a merger with another business. The same guidelines and HMRC's payroll error guidance list other routes to a duplicate that often travel with an ID change: sending starter details for someone who is not a new starter, treating a returning seasonal worker as a new starter, entering a new start date when moving to new software, reporting a correction to a start or leaving date on the FPS instead of just updating payroll records, and changing more than one personal detail, such as name and date of birth, on the same FPS.

HMRC links each Full Payment Submission to an existing employment using the employee’s personal details and the payroll ID. If the ID changes without the FPS flagging the change and quoting the old ID, and the year to date figures do not let HMRC match it another way, HMRC opens a second employment for the same person with the same employer. The usual result is an unexpected second tax code, a PAYE bill that does not agree with payroll, and a record that the employer cannot fix by sending more submissions.

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How does HMRC match an FPS to the right employment?

Every FPS carries, for each employee paid, the National Insurance number, name, date of birth, address, payroll ID (works number), tax code and year to date pay and deductions. HMRC’s guidance on the payroll ID field is that the ID must be unique, that a different ID is used if someone is employed again or holds more than one job in the same PAYE scheme, and that reusing a previous ID creates a duplicate record.

When an ID changes, two further fields come into play: the payroll ID changed indicator and the old payroll ID. HMRC’s RTI data item guide says the new ID overwrites the one held when both are completed. If the old ID is missing, HMRC cannot make a direct match and applies further matching rules to the financial data. In its worked examples the test is whether the previous year to date pay plus the pay in this period equals the new year to date pay. If it does, the record updates; if not, a duplicate employment is created.

Why does a changed payroll ID create a second employment?

HMRC’s own examples show three ways it goes wrong:

Change in month 1 without the old ID. Only one FPS is held for the new year, so there is no earlier year to date figure to test against. The match fails and a duplicate is created from month 1.
Change mid year with a keying error. The old ID is omitted and the carried forward year to date pay has two digits transposed. The arithmetic test fails and a duplicate starts from that month.
Reusing an old ID for a returning employee. This is the opposite problem. Two separate periods of employment are merged, so HMRC ends up with one end of year record based on the last FPS and ignores the earlier pay.

HMRC’s compliance guidelines GfC22 list the usual triggers for an ID change: changing payroll software, changing payroll provider, a restructure, or a merger with another business. The same guidelines and HMRC’s payroll error guidance list other routes to a duplicate that often travel with an ID change: sending starter details for someone who is not a new starter, treating a returning seasonal worker as a new starter, entering a new start date when moving to new software, reporting a correction to a start or leaving date on the FPS instead of just updating payroll records, and changing more than one personal detail, such as name and date of birth, on the same FPS.

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What tax code problems follow?

The data item guide sets out what HMRC’s system does when an FPS arrives with no start date or starter declaration and a change of payroll ID:

Employee’s existing record	What HMRC creates	Tax code effect
No current primary employment	A new primary employment	Code calculated automatically from the year to date earnings on the FPS
A current primary employment (often the original record with you)	A new secondary employment	A secondary code with no tax free allowances

So an employee who was on a normal code can suddenly receive a code with no allowances for the phantom job, while the original employment stays open. HMRC lists the knock on effects: an incorrect tax code, estimated pay problems, wrong end of year figures and calculations, a personal tax account that does not show the true position, and possible effects on benefit claims. GfC22 adds that the employee may pay the wrong amount of tax, National Insurance and student loan repayments and receive the wrong Universal Credit. The warning signs for the employer are an unexpected batch of tax code notices and staff asking why their code changed. The coding mechanics are covered in PAYE tax codes.

Does a duplicate affect the employer’s PAYE bill?

It can. GfC22 explains that a disputed charge arises when the PAYE due according to your payroll records does not match HMRC’s records, and that duplicate records can lead to paying too much or too little PAYE and to debt collection that should not have started. Where you dispute an amount, HMRC will usually pause debt recovery while it investigates, but you should keep paying any PAYE you do not dispute to reduce the risk of interest and penalties. How to compare the two sets of figures is set out in reconciling your PAYE account with HMRC.

How does an employer fix it?

Stop it repeating. On the next FPS keep the new ID, set the payroll ID changed indicator if it has not yet been reported, quote the old ID exactly as previously sent (including leading zeros) and make sure the year to date figures continue from the previous submission.
Do not try to cancel the phantom employment yourself. GfC22 is clear that duplicate records, or information linked to the wrong person, cannot be fixed by submitting a new FPS. The data item guide says duplicate records need clerical correction by HMRC because it is not an automatic process. Sending leaving dates or negative figures for the phantom record usually adds further mismatches.
Check whether HMRC has already corrected it. HMRC’s guidance on unexpected PAYE bills says incorrect bills and duplicate records caused by starter and leaver mistakes are usually corrected automatically, and that if the bill is still wrong by the 12th of the next tax month you can ask for help.
Use the online form. Requests go through HMRC’s Get help to correct an employer PAYE bill service. From 31 August 2025 employer PAYE disputes can no longer be reported through the helplines or webchat. You need the PAYE reference, the Accounts Office reference, the business’s Self Assessment or Corporation Tax UTR, the number of employees, and the year’s FPS totals from your payroll software for Income Tax, employer and employee National Insurance, student loan deductions and Class 1A. Each tax year needs a separate request, and HMRC aims to reply by email within 40 working days.
Keep staff informed. Tell affected employees that the extra code comes from a reporting error, and keep a list of the codes received so they can be matched up once HMRC has merged the records.

How might it look in practice?

Illustration only. A small company changes payroll software in April. The old system held an employee as payroll ID 0158; the new one imports the ID as 158 and treats the first payday as a new employment with a start date of 6 April. The month 1 FPS shows the new ID and no old ID.

Because it is month 1, HMRC has no earlier figures for that year to test, so the match fails. The employee’s original employment is still open as the primary job, so HMRC creates a secondary employment and issues a code with no allowances for it. Within weeks the employee queries the code and HMRC’s charge for the month no longer agrees with the payroll journal. The employer corrects the ID mapping, reports 0158 as the old ID on the next FPS, and submits the request through the online form with the payroll totals for the year.

How can duplicates be prevented?

Never reuse a payroll ID, even years later. The data item guide says IDs should be used only once, even for different people in later tax years.
Before any software or bureau change, map every old ID to its new one and test that leading zeros and prefixes survive the import. The full handover checklist is in changing payroll software or bureau mid year.
Do not send starter information for people who are already on your payroll, and check new starters’ names and dates of birth against official documents, as GfC22 recommends; the starter checklist page explains what to collect.
Leave the National Insurance number blank if you do not have it yet; never use a temporary or made up number.
On a change of legal employer, follow the succession or merger process rather than renumbering staff on the old reference; see PAYE when staff transfer under TUPE.

The fields involved are described in more detail in Real Time Information: FPS and EPS explained.

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Reviewed by Christine Anderson, Broker, Solar Protect. Last reviewed 24 October 2026. Part of Accountapedia, the Solar Protect guide to UK tax and accounting. This page is general information, not personalised advice.