The Federation of Motoring Clubs said some faced fourfold increases in road user charges, calculated on the basis of their legal carrying capacity rather than actual vehicle weight.
A typical converted bus with a gross vehicle mass of 14 tonnes but running on roads at an actual load of nine tonnes, could be charged $490 for every 1000km travelled, compared with $120 now.
That is if their owners have to pay their maximum potential loads based on existing road user charges, which are likely to be adjusted to some extent before the new regime is introduced in August.
The AA estimates that owners of about 217,000 diesel cars face fee rises, as do those of at least 23,000 motor homes.
Mr Stockdale acknowledged that fee scales could be changed to soften the blow, and urged the Government to do so in an announcement expected within a fortnight.
In announcing in last month's Budget a petrol tax rise of 2c a litre on August 1, the Government indicated it would impose a similar general rise on road user charges. But within the overall charging envelope, it wants to simplify the collection process by no longer allowing vehicle owners to estimate their loads.
They will instead be charged according to their maximum legal weights to cut out guess-work and outright revenue evasion.
It hopes to prevent annual losses to the system of at least $30 million, but is promoting the proposed changes as otherwise "revenue neutral", meaning that while some vehicle owners will pay more than now, others will end up better off.
Mr Stockdale urged the Ministry of Transport to either create a new category of vehicle to soften the impact on owners of motor homes, or to "tweak" the proposed changes to ensure they and those of small diesel cars would not be penalised unfairly.
Ministry officials were not available for comment yesterday.
But a spokeswoman said last week, in response to similar concerns raised with the Herald by courier firms, that it needed to change the definition of vehicle licence weights to simplify administration for both industry and government agencies.
She said it could be difficult for vehicle operators to predict weights to be carried on road trips, and the new system would close the door on those who deliberately under-estimated their loads in a bid to pay less.