The shutdown will also affect direct debits and automatic payments, which will be processed when Inland Revenue reopens. All payments will be treated as paid on the due date.
Inland Revenue spokesman Richard Owen said the final system changes were necessary to help support New Zealanders through Covid-19 and so it can stop using two IT systems.
"Completing business transformation now means it will be less risky and less complex than trying to make a change to help those affected by the pandemic while running two systems," Owen said.
"IR is making the upgrades over a public holiday, so systems are down for fewer business days."
Owen said taxpayers who want to apply for the third Resurgence Support Payment can do so prior to the shutdown, or any time after.
"Applications stay open until a month after all of New Zealand returns to alert level 1," he said.
The final upgrade to Inland Revenue will also bring Child Support into the new system.
Sue Gillies, Inland Revenue customer segment lead - families, said the changes will mean receiving parents will be paid more promptly.
"Currently Child Support payments should be paid to Inland Revenue on the 20th of the month and must be paid to customers by the 7th of the following month... [but] from November, we'll be able to pay Child Support payments to customers by the 23rd of the same month, as long as the payment has been made on time.
"Inland Revenue receives about a thousand new Child Support applications each month. From November, new liable parents [plus parents re-entering the system] who are working will have the Child Support deducted directly from their pay through their employer.
"We need to make sure these changes are live and being used successfully well before Christmas - a time of significant stress for people relying on those payments.
"This arrangement will be set up as soon as a Child Support application is received. We will also automatically set deductions with a liable parent's employer if they fall into arrears for two consecutive months."
Working for Families and Paid Parental Leave payments that are due during the shutdown will be paid early.
The improvements to myIR are hoped to simplify the way information is presented for customers, including visibility of their obligations and payments, as well as allowing users the ability to register online and advise of any changes in circumstances.
