What the payroll calculator will not work out
The South African pay situations Achekam's payroll calculator leaves to a person, such as lump sums and backdated pay, and how a bureau should handle each.
By Achekam · · 4 min read · For Accountants & audit firms in South Africa
Ordinary months are easy. Salaries, overtime, a medical aid deduction, PAYE, UIF and SDL: any decent payroll system gets those right once it is set up. The months that test a bureau are the unusual ones. A long-serving employee is retrenched. A wage agreement is signed with increases backdated several months. Someone resigns and cashes out a retirement benefit through the employer.
Those are the months where a confident-looking figure from software does the most damage, because nobody thinks to question it and the employee's tax comes out wrong.
Achekam's South African payroll calculator takes a clear position on these cases. Where it cannot work out the right answer, it says so instead of producing a figure.
The three cases it leaves to you
Each pay run works out gross pay, PAYE, UIF and SDL for every employee. The calculator does not handle three situations:
- Lump sums without a directive. Many lump-sum payments are taxed according to a directive from SARS, not the ordinary tax tables. Without a directive, the calculator does not guess.
- Backdated pay. Increases or arrears that relate to earlier periods raise questions about which tax year and which months they belong to.
- Retrenchment packages. Severance benefits have their own tax treatment, which depends on facts about the employee and the payment.
In each case the run returns a warning instead of a figure.
Directives you can record
For the first case there is a route inside Achekam. SARS tax directives (IRP3) can be recorded against the employee and applied to the run. Once the directive is in hand, record it, apply it, and the run reflects the tax SARS has specified.
The practical lesson for a bureau is timing. A directive has to be applied for and received before the payment is processed. When a client mentions that an employee is leaving with a payout, the directive application should start that week, not on pay day.
Warnings instead of figures
For backdated pay and retrenchment packages, Achekam does not supply the figure. The bureau works out the treatment itself, with the employee's history, the client's agreement and the relevant SARS guidance in front of it, documents how it reached the answer, and keeps that working with the run's records.
That may feel like a gap. It is a deliberate one. A wrong figure that looks authoritative gets approved and paid; a warning makes a person stop and think. Payroll software that guesses at these cases shifts the risk onto the bureau without telling it.
A worked example in words
A manufacturing client signs a wage agreement with an increase backdated to the start of the agreement period. The bureau captures the new rate for the current month, and the run raises a warning about backdated pay. The payroll officer works out the arrears for each affected month, decides with the reviewer how they should be treated for tax, records the reasoning, and only then completes the run. The approver, who did not prepare the run, reads the working before approving.
Corrections after approval
Until a run is approved it can be recalculated as often as needed. On approval, variable inputs are frozen, and from then on the run is corrected only by a correction run.
That matters for these unusual cases in particular. If a retrenchment package is processed in one month and the directive arrives later with a different figure, the original run stays as it was paid, and the difference goes through a correction run. The history of what was paid, and what was corrected, stays intact.
The usual separation of duties applies to correction runs as to any other: the person who prepared a run cannot approve it, and nobody can approve a run that pays themselves.
Confirming the tax table each year
There is one more thing the calculator will not do: assume the tax rates. Achekam's PAYE calculation has no tax rates written into it. A pay run is refused until a named person at the firm has confirmed that year's tax table, with a note of what they checked.
The tables ship pre-loaded but unconfirmed, and confirming one creates the firm's own copy. A South African tax year runs from 1 March to the last day of February and is named for the year in which it ends. For payroll paid on or after 1 March 2026, a firm must start its own 2027 table, which it can begin from the 2026 figures, and confirm it against the SARS tables before running payroll. No 2026/27 table ships with Achekam. Check the rates against SARS's published tables at the time you confirm them, because rates and thresholds change. SARS's employer guide on employees' tax for 2027 sets out the individual tax tables, rebates and thresholds announced in the 2026 Budget, and how employers must deduct PAYE.
A checklist for unusual payments
- Ask each client to tell the bureau about resignations, retirements, retrenchments and wage agreements as soon as they are known.
- For any lump sum, apply for the directive immediately.
- Record and apply directives in Achekam when they arrive.
- For backdated pay and retrenchment packages, prepare a written working and have a reviewer agree it before the run is approved.
- Use correction runs, never edits, for anything found after approval.
- Confirm the tax table before the first run of each tax year.
How each client is set up as its own employer is covered in running clients' payroll as separate employers. Unusual payments also tend to surface missing employee details; see clearing missing employee details.
When a warning appears on a run, treat it as the calculator handing the decision back to a qualified person, and make sure your bureau knows who that person is before the next one arrives.
General guidance only, not advice on your own circumstances. Tax and payroll rules change: check the current position with the authority or your adviser.
