Medical absences in the SME: sick leave, paid leave and how to manage them without errors

An employee calls at eight in the morning: they are ill and not coming in. From then on the company has to decide what kind of absence it is, what document it may ask for, how to reflect it in the working-time record, what to tell the accountant for payroll and what to report to Social Security. Medical absences are the most frequent incident in any workforce and, since 2023, when workers stopped handing their sick note to the company, also the one that raises the most questions. This guide sorts out the types of absence, what changed with Royal Decree 1060/2022, what the company can and cannot do, and a process for handling them without errors.

Types of medical absence

Not all health-related absences are the same, and treating them the same is the first mistake.

• Sick leave (temporary incapacity). The worker cannot work and a doctor from the public health service or the mutual insurer issues the sick note. It may be for a common contingency (common illness or non-work accident) or a professional contingency (work accident or occupational disease), and the payment regime differs: we explain it in who pays for sick leave and in who pays for sick leave after a workplace accident.
• Paid leave under article 37.3 of the Workers’ Statute. Since the 2023 reform, five days for serious accident or illness, hospitalisation or surgery without hospitalisation requiring home rest of the spouse, partner or relatives up to the second degree; and the time needed for prenatal examinations and childbirth preparation. These are justified, paid absence days, not sick leave.
• Absence due to family force majeure. Up to four days a year, paid according to the collective agreement, for urgent family reasons related to illness or accident that make the worker’s immediate presence indispensable (article 37.9).
• The worker’s own medical appointments. The Workers’ Statute grants no general paid leave for going to the doctor; it depends on the collective agreement, which often sets a number of hours a year or requires a certificate. If the agreement says nothing, it is time to be made up or deducted, unless agreed otherwise with the company.
• Unjustified absence. The worker is absent and provides neither sick note nor certificate. It is the only one that may have disciplinary consequences, and it must be documented as such.

Classifying each absence correctly decides everything else: whether it is paid, who pays it, whether it counts as working time and which document proves it.

What changed with Royal Decree 1060/2022

Since 1 April 2023 the sick-leave circuit works differently:

• The worker no longer hands the sick note, confirmation note or discharge note to the company. The health service or the mutual insurer give it to them and report it electronically to the National Social Security Institute (INSS).
• The INSS notifies the company of the note’s administrative data electronically, no later than the first working day after receiving it.
• The company reports to Social Security, through the RED System and within a maximum of three working days from receiving the sick note, the economic data that fall to it (contribution base, job, among others).
• Notes are issued according to the doctor’s estimated duration: in very short processes, under five days, sick leave and discharge may go on the same note; in short ones, five to thirty days, the first review is at seven days and subsequent ones every fourteen; in medium ones, thirty-one to sixty days, the first at seven and then every twenty-eight; in long ones, from sixty-one days, the first at fourteen and then every thirty-five.

In practice, the company learns of the sick leave from the worker, who is still obliged to say they are not coming in, and confirms it through the INSS notification. What it cannot do is demand the paper note as before.

What the company can and cannot do

• It can ask the worker to notify as soon as possible and to provide a certificate for absences that are not sick leave (medical appointment, leave for a relative’s hospitalisation), in the form set by the agreement.
• It cannot ask for the diagnosis. The note it receives does not include it and the certificate for an appointment need not either. Health data are special-category data and the company only needs to know that the absence is justified and how long it lasts.
• It can verify the state of health through an examination by medical staff (article 20.4 of the Workers’ Statute); if the worker refuses, they may lose the company-paid supplements, not the benefit.
• It cannot dismiss for justified absences. The objective dismissal ground for absenteeism in the former article 52.d) was repealed in 2020; justified absences due to illness are not grounds for dismissal.
• It must reflect the absence in the working-time record as such, not as time worked or as an unexplained gap, and inform whoever calculates payroll of each absence with its type and dates, because payment varies with the type, the day of the sick leave and whatever the agreement improves.
• It must retain certificates and communications for as long as employment and data-protection rules require, with restricted access.

A process that avoids errors

1. Notification. The worker reports the absence through the agreed channel on the first day. It is recorded with date and time.
2. Classification. Whoever manages staff assigns the type: sick leave for common or professional contingency, article 37.3 leave, family force majeure, medical appointment under the agreement, or unjustified absence.
3. Certificate. For absences that are not sick leave, the worker attaches the certificate within the period set by the agreement. For sick leave, the company waits for the INSS notification and keeps the record.
4. Reporting to Social Security. The economic data of the sick leave are sent through the RED System within three working days.
5. Working-time record and calendar. The absence appears in the record with its type and in the team calendar, so shifts and cover can be reorganised in time.
6. Payroll. At month end, the list of absences with type and dates goes to the accountant or the payroll program, without gathering it from emails and messages.
7. Follow-up. In long sick leave, note the expected review dates and the discharge date; in repeated unjustified absences, document them in case action is needed.

How LapsoWork solves it

LapsoWork’s leave and absence module is designed so this process does not depend on anyone’s memory:

• Absences and sick leave with their own types: medical, unpaid, paid leave, with the types your agreement sets.
• Request from the app with the certificate attached, and approval or recording by the manager with automatic notification.
• Shared calendar by team or site, to see cover before someone else is missing.
• Complete history: each absence is recorded with date, type, status and who handled it, auditable whenever needed.
• Exportable report to Excel for the accountant and for management, with the month’s absences per person and type.
• Link with time tracking: the absence is reflected in the working-time record, with no gaps or invented hours.
• Certificates in the document manager, with restricted access and orderly retention.

It is included in the Basic plan, at €2 per employee per month, together with time tracking and payslip distribution. Details are on the leave and absence software page and on our pricing page. And to measure whether absenteeism improves, the human resources metrics that come out of the system itself are the starting point.

Frequently asked questions

Does the worker have to hand the sick note to the company?

Not since 1 April 2023. Under Royal Decree 1060/2022, the health service or the mutual insurer report the note to the INSS, which transmits it to the company electronically on the first working day after. The worker is still obliged to say they are not coming to work, but not to provide the paper note.

Can the company ask for a certificate for going to the doctor?

Yes, in the form established by the collective agreement, which is what regulates whether the worker’s own medical appointment is paid leave, how many hours a year and with what justification. The certificate need not include the diagnosis, and the company cannot demand it.

Can a worker be dismissed for being absent a lot due to illness?

Not for justified absences. The objective dismissal ground for absenteeism in the former article 52.d) of the Workers’ Statute was repealed in 2020. Unjustified absences may have disciplinary consequences under the agreement, which is why each absence should be documented with its type.

What deadline does the company have to report sick leave to Social Security?

Three working days from receiving the sick note, through the RED System, to transmit the economic data that fall to it. It receives the note’s administrative data from the INSS electronically.

How is a medical absence reflected in the working-time record?

As an absence, with its type, not as time worked or as an unexplained gap. The record must distinguish sick-leave days, paid leave and unjustified absences, because each is treated differently in payroll and before the Labour Inspectorate.

Conclusion

Managing medical absences in an SME means classifying each absence correctly, meeting Social Security deadlines, asking only for the appropriate document and recording everything in the working-time record and payroll. Since 2023 the company no longer receives the note from the worker, so order has to come from the process itself, not from paper. If you want that process to live in your employees’ app rather than in a messaging group, try LapsoWork free for 30 days.