Container Centralen, which runs the European Danish trolley system, is asking retailers and growers to pay for £400 scanners, which are required to authenticate trolleys with radio frequency identification (RFID) tags being introduced on 10 January.
But some big firms are receiving free scanners from the company. Container Centralen UK managing director Phil Squance said the organisation would not pay for free scanners, except for around six of its "largest customers".
Retailers said they feared chaos if the system does not bed in as planned and predicted that a two-tier system would emerge. Squance said the two-tier system already exists, but he "can't see it developing further", adding: "All we are doing is making it clear where the division between the pools is."
When asked whether he could guarantee the system would not collapse at peak times this spring, he said he could not. "There can be no reassurance. If users of the pool do not put defences in place then there is nothing Container Centralen can do to reassure people."
Dobbies head of horticulture Neil Fishlock said: "There is uncertainty in the industry over this issue. The costs to our business are likely to be extremely high and we're reviewing on a weekly basis what is being asked by Container Centralen."
Fresh@Burcot Garden Centre owner Nicci Gow said: "As a small retailer in this industry I feel that this is the biggest issue to hit us since Sunday trading and the national minimum wage.
"We have Easter Monday and the May Day bank holiday with only four days in between. I can almost hear myself praying for bad weather to avoid the meltdown in plant supply that could happen if we run out of trolleys."
Alton Garden Centre director Andy Bunker said the new system was like a "tax", adding that it would stop early and late deliveries when no staff were at the centre.
Growers and garden centres argued that a two-tier Danish trolley system was likely to emerge. Some people in the supply chain called for an alternative to Container Centralen's system. It currently has 1,500 contracted UK customers for its trolleys.
Transflora transport manager John Bunting said: "If they want us to police their system they should provide us with the tools free of charge. There is a great opening to launch a rival system with lower rental costs and perhaps a tariff of equipment repair charges."
The electronic tagging is designed to keep the system free of counterfeit trolleys. It will bring down customers' contract costs but will mean initial outlays of £400 for tag scanners and longer delivery times as trolleys are scanned.
Many smaller retailers are refusing to sign up, which will mean nurseries that want to supply them will have to use rogue "DC" trolleys. Baginton Nurseries managing director Will Lamb said 10-15 per cent of his customers would only deal in non-tagged trolleys.
Squance added that tests had shown there should be no change in supply change timings and Container Centralen only wanted to protect the EUR250m trolley pool.