Sick leave on your payslip: deduction and Social Security pay

If you were on sick leave, your employer can deduct those days on your payslip. On those days Social Security pays you instead, from the 4th day. You get it by bank transfer or postal order and can track it in Segurança Social Direta.

Why your employer deducts sick leave days

An absence due to illness is a justified absence (Art. 249(2)(d) of the Labour Code). Your employer cannot mark it as unjustified or punish you for it.

But justified does not mean paid. Art. 255(2)(a) says an absence due to illness loses pay when you are covered by Social Security sickness protection. On those days your salary is replaced by sickness benefit, paid by Social Security.

So the employer deducts and Social Security pays. These are two different lines: one on your payslip, the other in your bank account.

[It depends on the case:] some collective agreements and individual contracts oblige the employer to pay a top-up. Ask HR for the text.

What about your day off? Marta's example

Marta thinks Sunday should not count, because she never works that day. The 7 day deduction is, as a rule, correct:

1. The sick note covers 7 consecutive days, day off included.
2. Social Security counts those days consecutively, weekends included. In the example in the Practical Guide on Sickness Benefit, a sick note that starts on a Thursday is paid from the following Sunday. The daily reference pay is worked out by dividing by 180, that is, 30 days a month.
3. [Common interpretation:] the monthly salary pays for the whole month, rest days included. So the employer deducts the same 7 days that Social Security covers.

The numbers:

[Common interpretation:] the formula salary / 30 x days is the most common. If your employer uses another one that gives more, or deducts days outside the sick note, ask for an explanation in writing.

The first 3 days and the exceptions

Sickness benefit only starts on the 4th day (Decree-Law 28/2004, Art. 21(1)). The first 3 days are the waiting period (days with no benefit). As the employer does not pay either, you lose your salary for those days.

There is no waiting period for (Art. 21(6)):

• Hospital admission or outpatient surgery.
• Tuberculosis.
• An illness that starts during parental benefit and continues after it.

Two more details:

• If you worked part of the 1st day and your employer paid that day, it does not count towards the 3 days (Art. 21(4)).
• If you first used the SNS 24 self-declaration of illness, those days count towards the 3 waiting days (Art. 21(7)).

The full sickness benefit rates are in the 2026 sick leave payment table.

When Social Security pays

The Social Security Practical Guide on Sickness Benefit gives no payment deadline. So we will not promise you a day.

What you know for sure (Practical Guide on Sickness Benefit):

1. You do not have to apply. The benefit is processed automatically when the health service sends the sick note to Social Security electronically.
2. Paper sick note? If it cannot be sent electronically, you hand it in to Social Security within 5 working days. If you hand it in later, you keep the right, but you are only paid from the day you hand it in, minus the 3 waiting days.
3. How you get paid: by bank transfer or by CTT postal order to your address.
4. Where you track it: in Segurança Social Direta you see the amount and the payment status.

Before worrying about a delay, check two things in Segurança Social Direta:

• Is your IBAN correct? Register or change it under Profile > Bank account. It waits for validation and you get a message once it is confirmed.
• Does the sick note show up? If not, talk to the doctor or health centre that issued it.

If your sick leave was a long time ago and there is no sign of payment, contact Social Security through Segurança Social Direta or the Linha Segurança Social (210 545 400 or 300 502 502, working days from 9:00 to 18:00).

The deduction looks wrong: what to do

1. Compare dates. Put the sick note and the payslip side by side. The deducted days must fall inside the sick note period.
2. Redo the maths. Base salary / 30 x days. The payslip must show the deductions and the period it covers (Art. 276(3)). See the payslip guide.
3. Ask in writing. An email to HR with a copy of the sick note is enough.
4. Swap for holiday. If you lose pay on days without benefit, you can swap that loss for holiday days above 20 working days. You must tell your employer expressly and they cannot refuse (Art. 257(1) and (3) and Art. 238(5)).
5. Complain. If your employer does not correct it, you can file a complaint with ACT. A pay claim only expires 1 year after the day after the contract ends (Art. 337(1)).

The full list of absences that lose pay is in justified absences: when you lose pay.

In short

Deducting sick leave days on your payslip is, as a rule, legal. Your day off counts if it falls inside the sick note. Social Security pays you for those days from the 4th day. Check your IBAN and track the payment in Segurança Social Direta.