The IRD deems that all salary and wages are taxable in the year in which payment was made. This is irrespective of when the work was or will be performed.
The Batch Due Date you use in Generate Payments determines the tax year in which the pay falls, as this flows through to Payday Filing as the Payment Date.
If you have a Period End date that falls on or after 1 April, but you pay your employees on or before 31 March, and use 31 March (or earlier) as your Batch Due Date, you will need to change your Period End date to be on or before 31 March.
For example, a group of employees are paid on 31 March for work performed from 26 March to 2 April. The normal Period End date is 2 April. The Period End date must be changed to 31 March (or earlier).
If the Period End date is on or before 31 March, but you pay your employees on or after 1 April and use 1 April (or later) as your Batch Due Date, then the Period End date must be changed to 1 April or later.
When you perform the End of Pay process, you adjust your next Period End date to be in line with your regular Period End dates.