The settlement includes an admission of guilt and a penalty of nearly $4.2 million.
SkyCity admitted to breaches from 2018 to 2023, and said they largely related to historical matters.
The agreement is subject to approval by the High Court.
Last week, SkyCity agreed a near $74m settlement with Australian authorities for breaches of anti-money laundering laws at its Adelaide casino.
The New Zealand Internal Affairs proceedings began in February 2024.
SkyCity executive chair Julian Cook said regulators in Australia and New Zealand were "rightly holding SkyCity to account".
"Over the past few years, considerable progress has been made towards upgrading our anti-money laundering and countering terrorism financing systems," Cook said.
"This does not lessen the seriousness with which we take these breaches and we are disappointed that SkyCity is in this position."
Cook said it took its responsibilities in combating money laundering and terrorism financing "seriously".
"On behalf of the SkyCity Board and management team, I accept and apologise for these long standing failings," he said.
"We have fallen short of the standards we should hold ourselves to, alongside failing to meet the expectations of our regulators, customers, shareholders and the communities we are part of.
"We are committed to, and have begun, delivering the level of change that is required to meet these expectations."
With two regulatory matters now settled, SkyCity continued to face the threat of a temporary suspension of its local casino licence for alleged breaches of the host responsibility code.
