FSS end-of-year submission

Overview

As we head into the new year, all employers with an active PE number will be required to submit their end-of-year documents to the Commissioner for Revenue (CFR). While some might view this as an onerous task, Talexio aims to make this as easy a task as possible. Keep on reading for a step-by-step guide on how to do this. 

Manual submission

If you will be submitting more than 9 FS3 forms then you will need to submit the files via the CFR’s online portal. Employers submitting 9 FS3 forms or less have the option to either submit the files electronically, or to send them by post to the following address:

          Office of the Commissioner for Revenue
          FSS Section, Tiġrija Palazz Level 0
          Republic Street,
          Victoria VCT1015
          Gozo

 

Online submission

Before submitting these files, you need to ensure that the following is in place:

1. All your employees who have featured in at least one payroll in the submission year (and thus have an FS3 with your company) have a valid ID card number, residence card number or tax number saved in their profile under their details section.
   
   
2. All your employees who have featured in at least one payroll in the submission year (and thus have an FS3 with your company) have a valid Social Security number saved in their profile under their details section (employment field). 
   
   
   
    
3. Each employee’s name and surname are in line with those on their ID card/residence card. 
4. All payrolls for the year are locked and each payroll is assigned to an FS5 (for more information on this, click here). 
5. Make sure that the company's reporting details are filled in. For more information on this, click here.

Generating the End-of-Year documents

In the Payroll section, click on three dots and End-of-year wizard: 

Now go through the following five steps:

1. 1. Electronic Lodgement

   

   The first step is to download the F3 and SSC files required to be uploaded to the CFR online portal.
   

   You can also click on the provided link to access the CFR portal directly from here. 

   If you are submitting the end-of-year documents for your own company, you will need to ensure that you have a CFR03 form. If you are a tax practitioner and you are submitting the end-of-year documents on behalf of a company, then you will need to ensure that you have a CFR02 form. 

   From the CFR portal, click on submit FSS files. Here you will be required to fill in the data in your FS7 (such as total gross emoluments, total tax deductions, etc.). You will also be able to upload the F3 and SSC files from here. 

   After doing so, you may click Test to check whether the submission will be accepted or not. Should it yield successful results, then you can proceed to pressing Submit.

   If the test results in some errors, then you will need to fix them and try again. 
   
    

2. 2. FS3s

   

   The next step is to generate the FS3s of each employee who worked with your company during the year. Here you have the option to download the FS3s, to save them to the employees' documents section on Talexio, and to email the FS3s. Should you wish to check them out before sending them to your employees, you will need to untick the checkbox next to 'Email'. 

   Please note that for employees who were terminated during the year and have already been emailed their FS3, the 'email' option will be automatically unticked. You may, of course, choose to tick it again. 

   For more information on how to generate FS3s, click here. 
   
    

3. 3. FS7

   

   Here, you may download the FS7 (a document which aggregates all your company's FS5s in a year), save it to your documents section and send it to yourself via email. Please note that the FS7 will be saved in the documents section and sent via email to the user who executes this action and not to other employees. 
   
    

4. 4. FS7 Submission Report

   

   Here, you can download the electronic lodgement report.
   
    

5. 5. Done
   
   

Testing your submission

You also may test your end of year documents for any errors by means of the FSS e-filing sheet provided by the CFR. Click on this link to access it. This will download an Excel spreadsheet. Here, you will be able to log in with your company's PE number and your E-ID (ID card number and E-ID password) by clicking on 'Personalise'. After inputting these details, the FS7 in the sheet will automatically populate (on the basis of the FS5s previously submitted to the CFR for this year). 
You will then need to navigate to the second and third tabs of the sheet.



Here you will be able to upload your F3 and SSC files respectively:


Once loaded, you will be able to see the data in these files, and you will be able to identify any mistakes (such as incorrect ID card numbers or employee names) and fix them through the sheet. Once fixed, you can click on 'Export FS3/SSC file' to generate the updated file. This can then be reuploaded to the CFR online portal. 

Please note that any changes done through this sheet must then be fixed on Talexio. Alternatively, you may use this sheet to identify the errors, then fix them directly on Talexio and re-generated the F3/SSC files from the end-of-year wizard again. 

Once the test on the CFR portal yields zero errors, you are ready to submit the files. Click on the submit button.

Common Mistakes and How to Fix Them

When testing or submitting lodgement files on the CFR portal, validation tests may fail if data is incomplete or formatted incorrectly. Below is a breakdown of the most common errors and how to resolve them:

• When a file fails the CFR validation test, the portal displays a results breakdown:

  • File Name / Header: Displays which file contains the error (F3 or SSC).
  • Error description: Explains what requirement or rule failed (e.g., "ID Number is invalid").
  • Line Number: Indicates the exact row in the lodgement file where the error is located.
  • Erroneous Field Name: Points out which specific field needs correction.
  • Erroneous Value: Shows the invalid value currently entered in that row.

  Note: The CFR portal may not display all errors at once; once you fix the initial set and re-test, additional errors may appear sequentially until all validations pass.

• Issue: The CFR portal rejects the uploaded files immediately upon upload.

  Cause: If you download the F3 or SSC file more than once, your browser automatically appends a number to the file name, such as 654321F3(1).23 or 654321SS(1).23. The CFR system only accepts the exact format [PE-Number]F3.[Year] and [PE-Number]SS.[Year] (e.g., 654321F3.23 and 654321SS.23).

  How to fix: Rename the downloaded file on your computer to remove any brackets or additional numbers before uploading, or delete previous versions from your Downloads folder prior to downloading from Talexio.

• Issue: "ID Number is invalid" or NI Number formatting errors.

  Cause:

  • ID numbers, Residence card numbers, or NI numbers contain extra spaces, brackets, or invalid punctuation.
  • The employee's surname does not match the surname registered with the CFR for that ID/Tax number (hyphens and special characters can also trigger rejections).
  • A Spouse ID/Tax Number was entered for an employee whose tax status is single, or spaces were entered in place of leaving the field completely blank.

  How to fix: Go to People > select the employee > edit Details. Ensure the surname, ID/Tax number, and NI number are formatted cleanly without spaces or symbols. Re-generate the lodgement files from the End-of-Year Wizard once updated.

• Issue: Emoluments, Tax, SSC, or Maternity Fund totals do not agree between files and the FS7.

  Cause:

  • Manual adjustments made in payrolls that were not reconciled across all reports.
  • Amounts containing negative values or cents where only whole numbers/standard formats are permitted.
  • Basic weekly wage declared as nil or left blank.
  • Number of SSC weeks does not agree with the employee's start/end dates, or exceeds 52 weeks (except in 53-week payroll years).

  How to fix: In Step 1 of the End-of-Year Wizard, click on Corrections to review and align any mismatched totals or manual calculation overrides. Alternatively, load the files into the CFR FSS e-filing spreadsheet to pinpoint exact numerical differences, correct them in Talexio, and re-export.

• Issue: Overtime tax or part-time tax calculations fail validation.

  Cause:

  • Overtime concession tax exceeds 15% of the concession overtime gross amount.
  • Qualifying part-time gross emoluments exceed the statutory €10,000 threshold or the tax deduction exceeds 10% (€1,000).

  How to fix: Verify whether the employee exceeded the concession limits during the payroll year. Any amount exceeding the thresholds must be adjusted to standard FSS tax rates.

• Issue: The End-of-Year Wizard blocks generation with an error message listing unassigned or unlocked payrolls.

  How to fix: All payrolls for the calendar year must be locked, and every single payroll must be assigned to its corresponding FS5 month (under Payroll > Reports & FS5 > Manage FS5s). Ensure no payrolls have been accidentally linked to the wrong month or left unassigned.

Congratulations, you have now closed off the year!

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