Traffic is banking up at a highway checkpoint at Auckland's southern border as police assess every vehicle travelling in and out of the region.

Motorists are being warned to expect long delays as police man highway checkpoints around Auckland's perimeter to enforce ramped up travel restrictions.

The change in alert levels from 1 to 3 overnight has seen the re-emergence of tough criteria for movements by road in and out of the region.

Big queues are now forming around Mercer heading south with traffic gridlocked along the Waikato Expressway almost back to Pokeno.

While police say there are no significant wait times, TimeSaver Traffic reports the Mercer road block is by far the region's biggest chokepoint leading to a long queue of traffic.

There are also short delays at Mangatawhiri and Brynderwyn.

All inter-regional travel to and from Auckland is now restricted to essential movements until Wednesday 11.59pm.

People wanting to cross will now need to carry official documentation issued by Government departments.

Eight checkpoints on the outskirts of Auckland will be stopping vehicles and questioning drivers, ensuring there is no non-essential movement through the region.

The New Zealand Transport Agency Waka Kotahi is warning people crossing the borders that they will have to wait.

"Please expect delays at State Highway police checkpoints operating 24/7 both north and south of Auckland every day until alert levels change.

"If you are travelling for essential purposes, or have obtained an exception for travel, please be patient at checkpoints with queues expected.

"Allow extra time for your journey and ensure you have necessary supporting documentation ready for presentation to help ease delays."

This time borders have been moved from the August lockdown where checkpoints were at Wellsford to the north and the Bombay Hills in the south.

The latest checkpoints are at Brynderwyn at the intersection of State Highway 1 and 12 at the northern end and south at Meremere on State Highway 1 (northbound, at Oram Rd), and Mercer (southbound, at Koheroa Rd) on State Highway 1 and Mangatawhiri (at Koheroa Rd) on State Highway 2.

It's causing a degree of confusion with residents living in the redefined checkpoint zones in Waikato and Northland unsure if they are in alert level 2 or 3.

Police say they will be highly visible across the region to provide reassurance and to educate people and ensure they are aware of the restrictions in place.

Commissioner Andrew Coster said this was not new territory for police or the public, and lessons learned from last time had allowed staff to mobilise quickly to respond to the change in alert levels.

"We will continue work with a graduated response, starting with education. We are once again asking the public be safe and abide by the alert level restrictions for their region.

"In Auckland, we will continue be visible and provide assurance to the community, and to checkpoints around the region's Super City boundaries."

Those needing to cross the border will need to seek permission with the government Unite Against Covid-19 website warning travel will be strictly limited.

People are being told to apply for an official business travel document.

"Exemptions will be limited to critical activity only. Requests will need to meet criteria and many requests will not be approved," the website advises.

For those wanting to travel across the border on a personal matter, the form will be processed by the Ministry of Health.

People are being advised to check whether they are eligible to travel between different areas of the country.