Clean Air Zones (CAZ) in Leeds and Birmingham will have significant costs for businesses, says the Freight Transport Association (FTA).
The organisation, which represents the transport industry, said Leeds Council has listened to a key FTA argument about restricting the size of zones where possible. But operators of larger HGVs will still face charges of £50 per day.
Van users will not be affected under the proposed scheme.
In Birmingham, the council has set out plans for a zone covering just the area inside its Middle Ring Road - smaller than the city-wide zone that had been feared by those responsible for deliveries to businesses within the centre of the city.
However, the proposals will cover all vehicles, so small businesses with vans as well as those with lorries will be affected. Vans as recent as three years old will be charged under the proposals.
FTA's head of UK policy Christopher Snelling, said: "CAZs only bring a temporary air quality benefit, bringing forward what was coming anyway. We need Councils to implement these zones with as much sensitivity to local businesses as possible. Leeds, especially, has listened to the concerns we and others expressed and reduced the impacts while still achieving their air quality objectives and we urge other cities to do the same.
"In both Leeds and Birmingham there will still be substantial impacts on small businesses, both from the costs of undertaking their daily work and shortening the lifespan of existing vehicles, that threaten their business models. CAZs need to be a last resort and as small as possible where they are used."
• Find out more about Clean Air Zones at Fleet Live 2018 on October 9-10 at the NEC in Birmingham. Visit the website.