A road-marking truck that flipped and burst into flames on Auckland Harbour Bridge has caused chaos across the motorway system this morning, with thousands of commuters left delayed by up to two hours.

The chaos has led to major congestion - now into the fifth hour - on the Northern Motorway and affected other motorways, particularly the Upper Harbour and Northwestern routes, as people tried to find alternative ways into the city.

Delays on the Harbour Bridge are to be expected again before lunchtime as authorities are set to shut down two left-hand southbound lanes to assess the state of the road surface.

A spokesman said at 10am the closure was due to happen after peak traffic had eased this morning.

"The lanes will be assessed and any necessary remedial action taken - like water blasting or spreading more absorbent material.''

The truck ended up upside down on the Harbour Bridge. Photo / Antony Gray

A median barrier on the right-hand lane is also going to be replaced after it was damaged by the crash.

"The bridge's moveable barrier will remain for now in its current configuration with five southbound and three northbound lanes.''

Motorists are advised to delay all non-essential travel on SH1 or avoid the area entirely.

The NZ Transport Agency even suggests: "Consider working from home.'' The other advice is to take buses into the city centre.

All lanes on the bridge are now open. But delays are still to be expected, authorities said.

At one stage, it was taking an hour and 48 minutes to drive from Greville Rd to the bridge - a distance of 15km.

The latest update said citybound traffic on the Northern Motorway was now moving well, with long queues starting to ease on surrounding on-ramps.

However, westbound traffic on the Upper Harbour Motorway (SH18) remains heavily congested from Brigham Creek Rd, in Hobsonville, to Lincoln Rd on SH16.

"Please use SH1 (Northern Motorway) to travel south and allow extra time for queues at all on-ramps.''

Emergency crews rushed to the Harbour Bridge after reports of the crash just before 5am.

Antony Gray heard the crash from his nearby home.

"It's right outside our house. We get a few crashes around there. I got up and saw it had started to smoke.

"The motorway [emergency] crews, police and fire engines were there pretty quickly,'' he said.

The Google traffic map shows delays (in red) across the northern motorway system.

Another witness, Janick van Well, said was heading towards the city, from the North Shore, when they came across a "ball of flames.''

"When we were coming up to the Harbour Bridge, we saw the above signs indicating that only the right most lane was open.

"When we got a bit closer, we saw some police cars and the over-turned truck and trailer in a ball of flames.

"The fire was so hot that even driving past, you could feel the wave of heat.''

There are significant delays on the Northern Motorway, citybound, with road authorities reporting just before 6.30am that it was taking 90 minutes to get into the city that way.

The bridge was down to one lane for more than an hour. By 6.45am, two out of the five southbound lanes were open. But the congestion stretches at least 15km.

Another witness described seeing a burnt-out truck as he drove past - as emergency crews continued to work at the scene.

The truck ended up upside down on the Harbour Bridge. Photo / Antony Gray

"I'm just passing the charred remains of a small truck. It's completely burnt out. It's upside down - nothing but a skeleton.''

He could not see any other vehicles that could have been involved; although he did see a tow truck pass through earlier, he said.

A photographer said according to police at the scene, the vehicle was a road-marking truck that had hit a centre barrier and flipped.

It is understood no one was injured. A St John spokeswoman confirmed they were called to the scene but then were not required.

The NZ Transport Agency is telling people to avoid the area completely or to delay travel.