The survey found that 43% of businesses were considering the change because about 80% believe charging will cost them more than £5,000 each year.
TransportEnergy public affairs manager Neil Wallis said: 'This gives a great opportunity to small businesses to gain a commercial edge by switching to the cleanest vehicles running on alternative fuels.
'Switching to cleaner fuels such as LPG, natural gas or electricity can help reduce two major problems: urban pollution and global warming. Traffic is the main cause of poor air quality in Britain's cities, causing health problems such as asthma and it contributes around a quarter of all carbon dioxide emissions.'
Only liquefied petroleum gas, compressed natural gas, hybrid petrol/electric and electric vehicles in the cleanest band four of TransportEnergy's PowerShift register can qualify for exemption from the £5 daily charge.
However, Transport for London (TfL) has warned that switching to alternative fuels is not a sure-fire way of avoiding the charge.
TfL has stated that the charge is to battle congestion, not encourage green transport, and that if too many vehicles were to switch to currently 100% discounted fuels, it would consider changing the exemptions.