Waka Kotahi National Manager Infrastructure, Andy Thackwray said Waka Kotahi's "first preference when disposing of residential homes is to sell the dwellings for relocation, rather than demolishment".
Thackwray said Waka Kotahi "is committed to ensuring that the residential properties which we own are safe, warm and dry for the people who live in them".
National's housing spokeswoman Nicola Willis said the costs showed the price of delays to building infrastructure.
"Delay costs huge amounts. Every day that you are delaying building a road that you still intend to build in future is a future costs," Willis said.
Willis applauded Waka Kotahi for actually meeting the Government's healthy homes standards, unlike Kāinga Ora, which owns the public housing stock.
Kāinga Ora has until July 1, 2023, to make sure all of its homes are compliant with the standards, unlike private landlords who must have their homes up to standard within 90 days of any new tenancy.
Act housing spokeswoman Brooke van Velden questioned why Kāinga Ora was given an extension for homes it planned to keep, while Waka Kotahi spent money doing up homes it might demolish.
"If Kāinga Ora, a state housing agency, doesn't have to have its homes up to standard for another two years, why didn't NZTA have the same exemption to save taxpayers $1 million dollars," van Velden said.
"This Government lacks common sense. It should take a step back and have a proper think about things before it rushes in with hard-earned taxpayers' money to solve problems that don't need solving," she said.
Transport Minister Michael Wood said he expected Waka Kotahi to be a good landlord," so it's appropriate that they are upgrading their houses to be warm and dry for renters".
"6,000 children are admitted to hospital every year for 'housing-sensitive hospitalisations'. Improving rentals will prevent kids from having to be admitted because of cold damp homes.
"Homes Waka Kotahi acquire can be held by them for a number of years, and some are relocated instead of being demolished.
"The amount they've spent upgrading them is also far lower than if they were fined for not doing so," Wood said.
It is not clear how long Waka Kotahi will own many of its homes. In some cases, like Wellington's long-awaited additional Mt. Victoria Tunnel, it has owned homes along the route since 1966.