Sustainable transport charity Sustrans said it will oppose plans to build a bus rapid transit route on part of the Bristol to Bath cycle track.
It said the route, which is used for 2.4 million walking and cycling trips, was the "right idea, wrong route".
"Sustrans supports high-quality public transport but not to the detriment of walking and cycling," a spokesman said.
Bus company First Bristol said taking buses out of traffic congestion had to be good for public transport.
A spokeswoman for the company added: ''First is working closely with all the local authorities involved in the bus rapid transit scheme.
"The aim is to help develop a system that will tackle issues of bus reliability and punctuality head-on.
"The scheme reflects our desire to help offer a practical alternative to people who currently use the car as their primary mode of transport.''
Bristol City Council said it had seen Sustrans' comments but said the council would need time to study the document in full before making a detailed statement.
Cllr Mark Bradshaw said the council understood concerns over the proposals for a rapid transit link.
"We will continue to work with cyclists, environmental and other partners in preparing more detailed proposals for how the cycle path can be enhanced and co-exist with the rapid transit link.
"It is possible that the rapid transit link could enhance use of the cycle path, making it easier for more people to use the path by combining a cycle and transit trip. We want to do all possible to improve the cycle path and make it easier to use.
"I also recognise we need to do more, working with our neighbouring authorities, to better explain rapid transit. I also want to make clear that no contracts have been awarded regarding the rapid transit operators."
About half the route between Bristol city centre and Emersons Green is currently the subject of a proposed rapid bus transit route.
Sustrans questioned the logic of building a rapid transit along much of its length and said the cycle path was "extremely popular".
It's spokesman added: "The charity believes that there are viable alternatives that should be explored, such as reallocation of road space into dedicated bus lanes.
"It also recommends extending existing walking and cycling routes that are already successfully reducing car traffic".