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The 27km four-lane motorway is being built through a public-private partnership, the Wellington Gateway Partnership (WGP), with CPB Contractors and HEB Construction sub-contracted to carry out the design and construction.
An NZTA spokesman confirmed to the Herald the email had been sent by CPB Contractors, which has been contacted for comment.
This morning, Maurice Davis, secretary of the Amalgamated Workers Union, which represents roading workers, said an apology was in order.
"We've reached out to our people and by all accounts the email said if you're not a New Zealander you have to come to work – and that is definitely something that we will never support," Davis said.
"Even if it was a mistake, you leave yourself vulnerable to misinterpretation where a person thinks because of their nationality, they have to come to work, and that is not on.
"I think there has to be an apology all-round - and maybe someone should get their arse kicked."
All workers were entitled to have Waitangi Day off unless it was explicitly stated in their employment agreement they could be required to work.
However, to discriminate against workers because of their race, ethnic or national origins - which includes nationality or citizenship - could be a breach of the Human Rights Act.
NZTA senior project delivery manager Andrew Thackwray said the agency recognised the importance of Waitangi Day for everyone in New Zealand, and they were "disappointed" by the email.
"It is important to us that anyone working for, or on behalf of, the [NZTA] is able to observe and celebrate Waitangi Day should they choose to, and we are addressing this directly with the contractor."
A spokesman for the Ministry of Business, Innovation and Employment said anyone working as an employee in New Zealand was covered by employment law, whatever their country of origin.