City bosses have criticised plans to ban all traffic access to the station as "irresponsible", claiming that they may take legal action against the operator.
Network Rail said its controversial £1 million anti-terrorism barriers would remain in place but would no longer allow taxis to enter the station from next Monday.
The dispute follows the death of 76-year-old Rev Tom Sinclair which has been linked to the faulty barriers.
Councillor Lesley Hinds, the city's transport convener, attended a "very amicable" meeting with Network Rail last week but there was "no mention" of the plan.
She said: "You cannot just do this without holding any discussion. They speak of increasing safety within the station, but what about passenger safety outside?
"The leave us no choice but to explore options to challenge them legally.."
The dispute with Waverley's operator started in January when Network Rail installed the security barriers without warning.
Council plans for a £1 million upgrade of surrounding safety measures and a new pedestrian crossing started this week. As of next Monday the station will be a vehicle-free zone and all taxis will be barred from entering.
David Dickson, Network Rail route managing director for Scotland, said: "We understand that removing taxis and private vehicles from the station does away with a convenience that people have become used to, however it is our job to balance convenience with the safety and best interests of all station users."