How to handle sick leave or a workplace accident

What is it for?

During sick leave or leave after a workplace accident, the company stops paying the pay for the days of leave, and the employee is paid by Social Security (illness) or by the insurer (accident). fiscaldoo handles sick leave in two parts:

• the absence, which all payroll profiles can see, with only the dates and a neutral name;
• the restricted record of the leave (certificate, who pays, waiting days), which only the View medical absence profile can open. Health data is a special category under the GDPR (RGPD).

Once the absence is approved, the month's payslip deducts the days of leave by itself.

When to use it?

• The employee has handed in a temporary incapacity certificate (CIT) for illness.
• The employee had a workplace accident and is off work.
• An extension of sick leave already recorded has arrived.

An absence for another reason (marriage, bereavement, unjustified absence) is handled in How to handle absences and lateness on the payslip.

Where to find it?

• The absence: Payroll › Prepare › Absences › New.
• The restricted record: Payroll › Prepare › Absences by incapacity (only shown to users with the View medical absence profile), or the Medical record button on the absence.

Before you start

• Who records it: Human Resources (HR profile, managing all absences) and with the View medical absence profile. This profile is closed by default, including for the system administrator; an administrator assigns it in Settings › Users & Companies › Users, on the user's form, in the Advanced settings tab, under Payroll PT — Medical absence › View medical absence, and the assignment is logged. Without it, HR records the absence but does not see the real type or the restricted record.
• Who gives the second approval: the Payroll Administrator (the absence's Validate button). HR cannot give it for a health absence.
• Who computes the payslip: the Payroll Processor, in the month's batch.
• The batch for the month of the leave has not been validated yet. Sick leave in a month already paid does not reach any payslip (see “Important notes”).
• Have at hand the CIT number and the dates, and know whether the employee has Social Security protection for illness.

How to use it

1. With the HR profile, open Payroll › Prepare › Absences and click New.
2. In Worker, choose the employee, for example Hugo Miguel Santos.
3. In Time Type, type impossibilidade and choose the type by its real name, which only the View medical absence profile sees:
   • Illness;
   • Accident at work;
   • Absence for exams, treatment or technical aids after a work accident.
4. In Dates, choose the first and last day of the certificate, for example 16/11/2026 to 20/11/2026. 5.00 day(s), Back to work on 21/11/2026 and First working day back 23/11/2026 appear.
5. In the Portuguese law: communication, proof and effect tab, fill in before approving:
   • Communicated at: the date the employee gave notice, for example 16/11/2026 (the field also stores the time, by default 00:00);
   • Proof delivered on: the day they handed in the certificate, for example 17/11/2026;
   • Social Security or insurance protection: Yes, No or Not said. With Not said, the second approval is refused (see “Common problems”).
6. Save (the absence is To Approve) and click Approve. It becomes Second Approval, with the Classification “Art. 249.º/2, alínea d: falta justificada.” (justified absence).
7. Click Medical record. The restricted record of the leave opens, already with the employee and the dates. Check:
   • Origin: it comes from the type (Common illness for Illness, Accident at work for the accident). The options are Common illness, Tuberculosis, Hospital stay or ambulatory surgery, Occupational disease and Accident at work. Choose only the origin, never the diagnosis;
   • Pays the benefit: Social Security, Insurer, Employer or Nobody (by default, Social Security for illness and the insurer for an accident);
   • Evidence: Electronic CIT (Social Security), Medical certificate, Hospital or health centre declaration or ADD.
8. In the Certificates tab, click Add a line and fill in Certificate number, Initial or prolongation (Initial or Prolongation), Issued on, Valid from and Valid until. In File you can attach a copy of the certificate. Save.
9. Ask the Payroll Administrator to open the absence (in Payroll › Prepare › Absences, Second Approval state) and click Validate. The Payroll Administrator does not have the View medical absence profile by default: they see the type as “Justified absence — impossibility to work (CT art. 249.º/2-d) — C” and the warning “Absence with a reserved justification: only the people authorised to see the reserved absences see the exact type.”. To validate they do not need to see the type, but if they want to read it or open the restricted record, a system administrator assigns them that profile (see “Before you start”). The absence becomes Approved and so does the restricted record.
10. With the Payroll Processor profile, open the month's batch (see How to process the month's payroll) and click Calculate. On the employee's payslip, check the Retribution lost by absences line.

What fiscaldoo calculates by itself

In the restricted record, the Effects (calculated) block shows:

• Days of leave: the calendar days of the certificate (5 in the example).
• Days of waiting in this leave: 3 for common illness; 0 for a workplace accident, tuberculosis and hospital stays. The waiting days decrease if you tick Start day was paid (the employee fell ill during the shift and the company paid the day), Began during a parental benefit or Days of self-declared illness.
• Suspends the contract (art. 296.º/1): unticked for this 5-day leave; fiscaldoo calculates it, you do not enter it.

Pending validation by a certified accountant: waiting days for common illness and the exceptions (Decree-Law 28/2004, art. 21), loss of pay only with illness protection (Labour Code art. 255/2-a), the day of the accident paid by the company and the sickness benefit paid by Social Security from the 4th day.

Illness example. Hugo Miguel Santos earns €1,250.00 and was on sick leave from 16/11/2026 to 20/11/2026 (5 working days). On the November payslip:

• Retribution lost by absences: 40.00 hours, −€208.33 (€1,250.00 ÷ 30 × 5). How was it calculated? says “5 day(s) of absence in the period”.
• Meal allowance: 16 days, €98.40.
• Gross €1,140.07; Social Security (worker) 11 % of €1,041.67 = €114.58; IRS withheld €27.00; Net to pay €998.49.

The company does not pay the 3 waiting days or the following ones. The sickness benefit is paid by Social Security directly to the employee and does not appear on the payslip.

Workplace accident example. Diogo Ferreira Lopes earns €1,150.00 and was on leave after a workplace accident from 09/11/2026 to 13/11/2026 (5 working days). The restricted record has Origin “Accident at work”, Pays the benefit “Insurer” and 0 waiting days. The November payslip deducts only 4 days (32.00 hours, −€153.33): the first day of leave, the day of the accident, is paid by the company. The other days are paid by the workplace accident insurer.

Recording sick leave does not create journal entries. The deduction reaches the accounting with the month's payslip.

Expected result

• The absence is Approved, with the Classification filled in.
• The restricted record is Approved, with the certificate, who pays and the waiting days. In the Absences by incapacity list, leave in months already paid appears as Processed.
• The month's payslip has the Retribution lost by absences line with the days of leave and fewer days of meal allowance.

Important notes

• Never write the diagnosis. Neither in the absence's Description nor in the restricted record's Note tab, where the field itself warns “Never clinical data.”. Every reading of the restricted record is logged.
• The restricted record's buttons. They only appear to those who can take that step. On a Registered record, the warning says that “o botão Validar só aparece a quem tem também o perfil de Recursos Humanos” (the Validate button only appears to those who also have the Human Resources profile). Users with View medical absence but without the HR profile have no buttons. After Validate, the record is Validated (HR), HR no longer has Approve, and the approval moves on to the Payroll Administrator (step 9).
• Fill in the communication and the proof before approving. If you change Communicated at, Proof delivered on or Social Security or insurance protection on an absence in Second Approval, fiscaldoo sends it back to To Approve without warning, and you must approve it again.
• Sick leave in a month already paid is not included in any payslip. Sick leave from 26/10/2026 to 27/10/2026, with October already paid, was approved without warning and the November payslip did not deduct it. Do not use the sick leave record to deduct a closed month: the adjustment is made by correcting that month's payslip, with the accountant.
• Extension. An extension is recorded as a new absence, starting the day after the previous one ends. In the restricted record of the new leave, the Continues field links it to the previous one.
• Illness verification. The restricted record's Verification of the illness tab stores the verification request to Social Security and the result (Law 105/2009, arts. 17 to 22). If the employee objects to the verification, tick Worker opposed the verification: the holiday days covered by the leave are no longer returned to the balance.
• Return to Social Security. Pending on-screen validation: how the days of leave appear in the monthly return to Social Security. The November return can only be prepared once the batch is paid, and in the demo the November batch is only computed.

Common problems

Typing “Doença” in Time Type shows nothing

• Symptom: typing Doen only suggests Leave to assist a child with a disability or chronic disease (arts. 52.º and 53.º).
• Cause: the search looks for the type's neutral name, even for users with the View medical absence profile.
• What to do: type impossibilidade and choose Illness or Accident at work in the list.

Time Type only shows the letters A, B and C

• Symptom: the types appear as Justified absence — impossibility to work (CT art. 249.º/2-d) — A, — B and — C, and there is no Absences by incapacity menu or Medical record button.
• Cause: the user does not have the View medical absence profile. The letter does not reveal the reason, on purpose.
• What to do: ask someone with that profile to record it, or ask an administrator for the profile.

On validating, “… is lost only if the worker has Social Security or insurance protection …” appears

• Message (seen by the Payroll Administrator): “Invalid Operation The retribution of “Justified absence — impossibility to work (CT art. 249.º/2-d) — C” is lost only if the worker has Social Security or insurance protection (art. 255.º/2) and nobody said whether Hugo Miguel Santos has it. What happened: the system does not guess. How to fix it: fill in “Social Security or insurance protection”.” Users with the View medical absence profile see the real type name here.
• Cause: the Social Security or insurance protection field was left at Not said.
• What to do: HR fills in the field on the absence, clicks Approve again, and the Payroll Administrator clicks Validate.

On saving the certificate, “Some required fields are empty” appears (or the line disappears)

• Message: “Some required fields are empty. Fill in the fields marked in red to be able to save.”
• Cause: the certificate line has no Issued on, Valid from or Valid until. A completely empty line disappears on saving, with no message; with only the number filled in, the message could not be reproduced.
• What to do: fill in the line's three dates and save.