How to fix missing clock ins without delaying payroll

Written by Roster Flow. Published 30 June 2026.

A missing clock in or clock out is a small problem on the day and a large one on payroll day. On the day, the supervisor remembers who opened and the employee remembers when they left. By the end of the fortnight nobody is sure, the approval deadline is an hour away and the choice looks like guessing or paying late.

Neither is necessary. The fix is a short routine: find the gaps within a day, confirm the times from more than one source, record the correction with a reason, and set a cut-off that leaves time to do it. To see how far hours have drifted from the roster, the roster vs actual hours calculator lines the two up.

Why clock ins go missing

• The rush at the door. The opener walks in, turns on the machines and serves the first customer before thinking about the clock.
• A flat phone or no signal. The employee meant to clock in and could not.
• Clocked in, never out. The close ran late, the lights went off and the shift is still open the next morning.
• The wrong shift or venue. The clock in landed against Tuesday’s shift instead of Wednesday’s, or against the other site.
• A shift that was not on the roster. Somebody came in to cover and there was no shift for their clock in to attach to.

Each one leaves a different gap, which is why it helps to know which kind you are looking at before you start asking questions. A missing clock out with a closing checklist signed at 22:20 is a five minute fix. A shift with no times at all and no other record is a conversation.

Fix the record, not just the pay

It is tempting to type in the rostered times and move on. The problem is that the timesheet is part of your time and wages records, and those come with rules. The Fair Work Ombudsman sets them out: records must be kept for 7 years, they cannot be changed unless the change corrects an error, and they cannot be false or misleading. For a casual or irregular part-time employee paid by the hours they work, the hours worked have to be recorded.

So a missing clock in is a record to correct, with the best evidence you have, not a gap to fill with whatever the roster says. Correcting it properly also protects you. An employee can ask to see their records, and the Ombudsman notes that an employer who has not kept records may, in some cases, have to prove to a court that they did not underpay someone.

Find the gaps the same day

The cheapest time to fix a missing clock in is within a day. Make a short check part of the manager’s close, or the first job the next morning, and look for three things:

• A rostered shift with no clock in
• A clock in with no clock out
• A clock in with no rostered shift behind it

Five minutes a day beats an hour on payroll day, and the questions are easier to answer while the shift is fresh. If you want to see the pattern over a longer stretch, the rostered versus worked hours calculator shows where worked hours and rostered hours part company.

What counts as evidence

No single record settles every case, so line up what you have. Two sources that agree are usually enough to enter a time with confidence.

Fix a missing clock in, step by step

1. Check what you already havePull up the roster, any clock out or clock in that did record, and the checklists or till log for that shift.
2. Ask the employeeSend a short message the same day: "No clock in for Tuesday. What time did you start?" Ask an open question rather than suggesting the rostered time.
3. Confirm with the supervisorCheck the employee’s answer against what the supervisor saw, or against another record from the table above.
4. Enter the times with a reasonAdd the missing time and a note: what was missing, what the time is based on, who confirmed it and when. For example: "Clock in missing, phone flat. Start 6:00 confirmed by Sam, 15 October."
5. Approve before the cut-offApprove the corrected timesheet so the hours sent to payroll are the checked ones. Approving timesheets covers the approval step.
6. Tell the employee what was enteredA one line reply closes the loop and gives them the chance to say if something is wrong before pay day, not after it.

When the times cannot be confirmed before pay day

Sometimes the employee does not reply and the supervisor is not sure. Do not leave the shift out of the pay run while you wait. Several awards say wages must be paid for a pay period according to the hours worked in that period, or averaged over a fortnight: the Fast Food Industry Award in clause 16.2 and the General Retail Industry Award in clause 18.2, for example.

If you know the shift was worked but not the exact times, pay the hours the evidence supports, usually the rostered shift when the supervisor confirms attendance, and note that the times are unconfirmed. When the employee comes back with different times and they check out, pay the difference straight away rather than leaving it for the next pay run, and note which shift the adjustment belongs to.

Do not take anything off pay as a penalty for forgetting to clock in. The Fair Work Ombudsman notes that there are only limited situations in which an employer can make a deduction from an employee’s pay. Repeated missing clock ins are a conversation about the routine, not a pay matter.

A worked example: three gaps in one fortnight

A cafe pays fortnightly. The pay period ends on Sunday, timesheets must be approved by 12:00 on Monday, and pay day is Wednesday. On the Monday morning check, the manager finds three gaps. Every shift of 5 hours or more had a 30 minute unpaid meal break, which was taken.

Mia’s shift is 8 hours less a 30 minute break, 7.50 hours. Josh’s is 6.5 hours less a 30 minute break, 6.00 hours. Priya’s 4 hour shift has no break. All three go into Wednesday’s pay: 7.50 + 6.00 + 4.00 = 17.50 hours. On Tuesday Priya replies that she stayed until 12:30 to finish the cake order, and the supervisor confirms it. Her Saturday becomes 4.50 hours, and the extra 0.50 hours is paid as an adjustment that week, with a note against the Saturday shift. The three shifts now total 18.00 hours, and nobody waited for their pay.

Set a cut-off that protects pay day

Most missing clock ins become payroll delays because the correction window is too short or nobody knows where it ends. Work backwards from pay day: when the period closes, when corrections are due, when timesheets must be approved. The payroll cut-off planner lays those dates out for weekly, fortnightly or monthly pay.

A few rules shape the calendar. The Fair Work Ombudsman says most awards and agreements set out whether employees are paid weekly, fortnightly or monthly, and if they do not, employees must be paid at least monthly. Pay slips have to be given within 1 working day of pay day. Some awards also limit the pay day itself: under the Restaurant Industry Award (clause 19.2), the Hospitality Industry (General) Award (clause 23.2) and the Registered and Licensed Clubs Award (clause 20.1), wages are not paid on a Friday, Saturday or Sunday except on termination, or on the Friday of a public holiday week if the employer and most employees agree. Under the General Retail Industry Award (clause 18.3), the regular pay day is notified in writing and can only be changed with 4 weeks’ written notice.

Casuals can be quicker still. Under the Restaurant Industry Award (clause 11.4) and the Hospitality Industry (General) Award (clause 11.5), a casual is paid at the end of each engagement unless weekly or fortnightly pay has been agreed. If that applies to anyone on your team, there is no fortnight to wait for, and a missing clock in has to be fixed the same day. Check your own award with the Fair Work Ombudsman’s Find my award tool.

Stop the same clock ins going missing

• Put the clock in where people arrive. Make it the first thing on the opening checklist, before the machines go on.
• Keep a backup. A clock in and out sheet by the door covers the day a phone is flat.
• Check daily. The same day check above catches the gap before anyone has forgotten the shift.
• Look for patterns. If the same person or the same shift keeps missing, it is usually the routine at that time of day, not the person.
• Keep breaks honest too. An open break is a missing clock in by another name; recording unpaid breaks covers how to handle it.

Roster Flow is built for this part of the week: availability and leave from staff phones, the roster published to everybody at once, clock ins that become timesheets, and approved hours sent to Xero, MYOB or a CSV file.

A checklist for missing clock ins

• Missing clock ins and clock outs are checked every day, not on payroll day
• Times are confirmed from at least two sources before they are entered
• Every correction has a note: what was missing, what the time is based on, who confirmed it
• The employee is told what was entered
• Unconfirmed shifts are still paid, and marked for follow up
• Later changes are paid as an adjustment straight away
• Nothing is deducted as a penalty for forgetting
• The correction cut-off leaves time before pay day

For the full run from roster to pay slip, the roster to payroll checklist puts these checks in order.

Sources

• Fair Work Ombudsman: record-keeping
• Fair Work Ombudsman: pay slips
• Fair Work Ombudsman: frequency of pay
• Fair Work Commission: Fast Food Industry Award 2020 [MA000003]
• Fair Work Commission: General Retail Industry Award 2020 [MA000004]
• Fair Work Commission: Restaurant Industry Award 2020 [MA000119]
• Fair Work Commission: Hospitality Industry (General) Award 2020 [MA000009]
• Fair Work Commission: Registered and Licensed Clubs Award 2020 [MA000058]
• Fair Work Ombudsman: find my award

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