Speaking to reporters in Tauranga this morning, Mr Key talked down the possibility of tolling in the near future, saying no commitment had been made and there were big technological hurdles to overcome.
"What we are saying is they are potentially an option," he said.
Mr Key was also at pains to emphasize that any direct charges were not meant to raise revenue.
"It's not about socking it to the consumer with more costs, it's about changing the behaviour of what they do."
Any tolls would differ from London's "congestion charge", which Mr Key described as "prohibitive".
In London, motorists are charged £11.50 (NZ$23.70) a day if they enter a designated congestion zone between 7am and 6pm.
A road pricing system in Auckland is more likely to be based on the Singaporean model, which has varied charges for the whole roading network depending on location and time of day.
Mr Key added: "In the event that we ultimately agree some years down the track to a more efficient road pricing it would probably come as we reduce petrol taxes."
Petrol excise is currently around 67c per litre, most of which goes into paying for transport infrastructure.
Labour's Auckland Issues spokesman Phil Twyford said today that road tolls would mean huge travel bills for Aucklanders.
The average commute in the city was 11.8km, which would amount to costs of between 70c and $10 a day under a tolling system, he said.
This estimate was based on modelling in the Government-council report, which suggested tolls of between 3c and 40c per kilometre travelled.
Transport Minister Simon Bridges said the prices used in the report were purely hypothetical and were only used to investigate the potential impact of road charges in Auckland.
"There is no basis at all at this incredibly early stage to make any assumptions," he said.
Last year, a small majority of Aucklanders supported tolls to fund transport projects during consultation on a long-term budget, but the Government blocked the idea, which requires legislation.
It is not yet known whether scooters and motorbikes would be exempted from road tolls, as is the practice overseas.