FlexiTime PAYE Service


IRD is introducing a new system for PAYE reporting called Payday Filing. From 1 May 2018 we will be moving all of our PAYE intermediary customers to Payday Filing and FlexiTime will no longer be a PAYE Intermediary. Please email [email protected] with any questions about Payday Filing.


If you're on the PAYE Service, FlexiTime is your PAYE intermediary.


How it works:

  1. When you finalise a pay, your Banking Payments Batch file will automatically download, or if you can't use batch files we'll email you your Payment Summary. It will include a PAYE payment to be made to FlexiTime’s Commercial Trust account. Upload your Banking Payments Batch file to your business banking account as normal, or pay the amounts shown on your Payment Summary.

  2. On or around the 5th of each month FlexiTime will email you a statement of account showing how much PAYE is owing for the last tax period and how much has been received. Normally these amounts will balance.

  3. By the 20th of each month FlexiTime will pay your PAYE to IRD and file your ir-Files on your behalf. You don’t need to do anything.


Important Notes:

  1. Don’t forget to complete your last PAYE payment and IRD Filing for the final tax period before FlexiTime takes this over. After that, we’ll take care of it for you.

  2. You must use the Banking Payments Batch file automatically downloaded from FlexiTime every pay date to transfer the PAYE total to the FlexiTime Commercial Trust account.

  3. If you can't use Banking Batch files, you must let us know. We'll set you up to receive your Payment Summary by email, and you must pay the amounts shown using the references provided.

  4. If you have not made sufficient payments into the FlexiTime Commercial Trust account for the filing period and fail to pay immediately upon notification, you will be de-linked from the PAYE Service. We will contact you by the 5th of the month to notify you of any shortfall.

  5. If you choose to no longer use FlexiTime’s PAYE Service or you are de-linked by FlexiTime, any payments made to the trust account and not already paid to IRD will be refunded and FlexiTime will cease to be linked to your company for IRD intermediary purposes.

6. If you are required to file twice monthly,  then you will not be able to use the PAYE Service.





Do I have to pay the full tax amount to FlexiTime each pay day?

Yes. It is a condition of using the PAYE service that you transfer the tax amount to the FlexiTime Commercial Trust bank account every pay date. 


What if there are multiple pays on the same pay date?

If two or more pays are processed with the same pay date, only the bank file for the last pay that was finalised should be loaded. 


What if I reverse a pay?

If you reverse a pay before you've loaded the Banking Payments Batch file to your bank, just create a new Banking Payments Batch file (Payroll > Reports > Bank files > Banking Payments Batch) and use this to load to your bank file.

If a pay is reversed after the payment is made to the FlexiTime Commercial Trust account, the amount paid will be refunded back to your bank account as listed on the company settings screen.  Account overpayments are refunded at the end of each month - please contact FlexiTime Support if you require an earlier refund. 

If you're not using the Banking Payments Batch file, or if you want to check the amounts owed to FlexiTime Trust for a pay, run the Pay Summary report and check the Payment Summary section. You can run this report for a pay by viewing the pay and clicking Options, or for all pays on a pay date by selecting Payroll > Reports > Pay Reports


What if I need to reverse a pay in a previous tax period?

Please email [email protected] for assistance.


What if I need to create a pay for a previous tax period?

Please email [email protected] for assistance.


What if I can't use the Banking Payments Batch file? 

If you are unable to use Banking Batch files, you must notify FlexiTime so that we can set up your account appropriately.

FlexiTime will automatically send you a payment summary each time you finalise a pay to assist you with making your payments. You must use the bank codes and references provided on this payment summary to ensure that FlexiTime can identify your tax payments. This will be emailed to the Contact Email address in your Company Settings.

You will be responsible for making manual payments to FlexiTime each pay day. Payment in full and on time is a condition of the PAYE Service, and failure to do so may result in your removal from the Service.


Can I set up an automatic payment to FlexiTime Trust?

No.  There are too many factors that can affect the total tax and deductions in a pay.  You need to pay the exact amount every pay date to ensure that your tax payments are correct and up to date. 


Do I need to provide a Letter of Credit from my bank?

No. FlexiTime will never take money out of your account, so we don’t require a letter of credit. You can sign up to our PAYE Service with a simple one-page form.


What are FlexiTime’s obligations as an intermediary?

Provided that we have received full payment from you for the tax period, as your PAYE intermediary, it is our responsibility to ensure your PAYE is filed and paid to Inland Revenue on time each month. You will not be liable for any penalties for late payment.


What if I already have a Tax Agent linked with IRD?

Inland Revenue can link FlexiTime as your PAYE Intermediary without changing your existing Tax Agent.


What if I'm already using a different PAYE Intermediary?

Inland Revenue will de-link your company from your current PAYE Intermediary when you are linked to FlexiTime.


What happens with tax periods before the PAYE Service starts?

When you start with the PAYE Service, we will advise Inland Revenue of the date and tax period on which FlexiTime becomes your intermediary. You will be responsible for filing and paying for previous tax periods. We will let you know what your remaining obligations are when you sign up to the PAYE Service.


What happens with the KiwiSaver KS1 file?

FlexiTime will file your IR348 and IR345 with IRD every month. You will still need to file any KS1 returns yourself.


If FlexiTime is my PAYE Agent, what happens when Inland Revenue sends me letters?

As your PAYE Intermediary, FlexiTime will receive all correspondence from Inland Revenue regarding your company's PAYE and employee tax deductions. We will scan and email a copy of any letters received to the Contact Email address on your Company Settings page in FlexiTime. You will need to take any action required by IRD. FlexiTime will not update your employee details.


What if I need to pay an employee cash?

If you need to make a cash payment to an employee, you will still need to record this in the pay. If you need to pay the employee their wages in cash instead of by bank transfer, you will still need to use the Banking Payments file to transfer the tax amount to FlexiTime.  Please email [email protected] if you need assistance.


How do I know what has been filed with IRD?

FlexiTime will send an email to your Contact Email address with details of the payment made for the tax period. You can also check your IR348 in FlexiTime for the current or past tax periods at any time.  Select Payroll > Reports > IRD Reports. Please do not file this return with Inland Revenue,  or they will de-link you from the PAYE Service.


IRD say I need to file twice monthly

PAYE Intermediaries can only file once monthly.   If IRD has requested that you file twice monthly,  you will not be able to use the PAYE Service. 


What if I want to stop using the PAYE Service?

If the PAYE service no longer suits you, you can stop at any time. Please contact FlexiTime Support to arrange this.


What happens if FlexiTime removes me from the PAYE Service?

If your company does not meet the conditions for the PAYE Service, FlexiTime may remove you from the service. You will be notified and any funds received by FlexiTime for the unfiled tax period(s) will be refunded to your bank account.

You can continue to use FlexiTime as your payroll system and file and pay your PAYE yourself. If you would like to use a bookkeeper or accountant to assist with this, FlexiTime has a number of partners you can contact.

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