Mohammed Bashir, of Boro Taxis, said the decision had been taken on economic grounds.
Teesside taxi operators were recently warned they could lose their licences for overcharging disabled passengers.
Middlesbrough Council believes the conduct breaches discrimination laws.
Mr Bashir said his company cannot afford to send an eight-seater minibus to pick up customers if it can only charge them the same price as it would an able-bodied person using a four-seater car.
'Morally totally wrong'
"The simple fact is if you order a car and four people jump in you are charged for a taxi. If you order an eight-seater minibus and eight people jump in you are charged for a minibus.
"If you order a minibus and there's only one person you will still be charged for a minibus because that's what you ordered.
"But because we are charging for a minibus we are breaking the law."
Mr Bashir told BBC Tees the decision was "morally totally wrong" but added it was "uneconomic" to continue carrying disabled passengers in minibuses.
Middlesbrough Council said it was looking into the matter and had written to taxi operators reminding them of their obligations under the Equality Act 2010.
Deputy mayor Dave Budd said companies "have a moral obligation to treat everybody the same".
Last month a report by the authority found wheelchair users were sometimes being charged up to double the standard fare.
Article from the BBC