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Higher charges will affect diesel-powered vehicles, and those weighing more than 3.5 tonnes.
Trucking companies are furious after the increase was announced on Monday night and came into effect yesterday.
Road Transport Forum New Zealand chief executive Tony Friedlander said the group, which represents about 80% of the country's commercial road transport operators, last year sought assurances from Transport Minister Annette King that operators would be notified of increased charges.
The forum received written confirmation members would be informed of changes.
"It is not just the increase. It's that it came without notice having received assurances.
"On top of the highest fuel prices in history, increases to the accident compensation levy and wage interest costs, it will do extreme damage to industry.
"Members have said they will have to pass costs as soon as they can.
This will be felt in provincial areas and cities like Dunedin which are very dependent on road transport," he said.
The increase was announced in a statement posted on the Government's website on Monday night.
No media statements were issued.
"The timing of this increase and the way it has been done mean the minister could not have done more damage to our industry if she had deliberately tried," Mr Friedlander said.
"She should not underestimate how angry our members and the industry are."
Mr Friedlander said the increase would inevitably mean higher costs for businesses and higher prices in supermarkets.
However, Ms King said the impact would be "relatively insignificant" and she did not expect any noticeable effect on consumer prices.
Ms King said the increases were introduced to defray costs of the national land transport programme.
Under the programme, $2.7 billion was allocated for transport activities in 2008-09.
This included about $791 million for state highway construction, $325 million for passenger transport services and infrastructure and $273 million for road policing.
"Without all road users paying their fair share, this level of investment cannot continue to be sustained," she said.
Charges for a 44-tonne truck and trailer unit which travelled 100,000km a year would increase to about $56,000, about $4000 more for operators, Mr Friedlander said.
Road user charges for transport operators in New Zealand were already 200% higher than those paid by Australian businesses using comparable trucks, he said.
Bus and Coach Association chief executive Raewyn Bleakley said members were "shocked and angry".
The "highest level of feedback" about the charges had been from tourism operators, she said.
"Tourist operators negotiate rates for services months in advance, and this increase will leave them screaming. This will be noticeable in places like Queenstown."
According to figures compiled by the association, operators of an 11-tonne school bus which travelled 17,000km annually would now pay about $250 more in road user charges.
A 10-tonne city bus which travelled 90,000km each year would incur an extra $1021 in charges a year.
Operators of a tour coach weighing 18 tonnes which travelled 70,000km each year would pay an extra $1330 and a 17-tonne long distance vehicle travelling 200,000km each year would incur $3730 in extra costs.