The minister said it was ridiculous for the Auckland Council to think it could use taxpayer-funded roads to raise its own funds.
The Government had said "no" to what was effectively a tax.
He also opposed congestion charges at peak hours, saying that internationally, congestion charges were used to deal with congestion, not to raise money.
Last year, the Transport Minister at the time, Steven Joyce, ruled out a regional fuel tax and had "significant reservations" about tolls and congestion charges.
Mr Brown, elected on a platform to build the city rail link, rail to the airport and rail to the North Shore, has struggled to get support from the National Government for the rail link and generate public debate on the funding issue.
A discussion paper on new funding sources, issued by Mr Brown in February, attracted only 161 responses and led to a consensus-building initiative.
The Government's position prompted left-leaning councillor and public transport champion Mike Lee to say yesterday that Mr Brown's best hope was a change of government.
Last night, Labour's transport spokesman, Phil Twyford, said the Government had control issues when it came to Auckland - first abolishing plans for a regional petrol tax, refusing to pay its share of the rail link and now ruling out other funding ideas.
Hitting Auckland's poorest people with tolls to travel to and from low-paid jobs prompted a council rethink on the consensus building group.
The make-up of the group, which includes business and property interests, came in for criticism by councillor Cathy Casey and others.
Dr Casey said the make-up of the group was an insult to low-income people, whose hourly rates of $13.50 would be eroded by tolls travelling to and from central city jobs.
She suggested that a Council of Trade Unions delegate join the sole low-income representative on the group, Donna Wynd of the Child Poverty Action Group.
Council chief executive Doug McKay, who is overseeing the consensus building group, said it was a good idea to broaden its make-up.
FUNDING FOCUS
* Motorway tolls.
* Congestion charges.
* Higher parking fees.