The firm has applied to demolish the Grandpont footbridge, near White House Road, and build a replacement for its ongoing track-electrification scheme.
But Oxford City Council’s West area planning committee has denied its approval, meaning the only remaining option is an appeal.
The local authority argues that replacement bridges should include ramps for the disabled and pushchair access, which Network Rail has not included in its plans so far.
Speaking after the decision on Tuesday night, committee chairman Oscar Van Nooijen warned that if Network Rail continued to fight the council it could strain the relationship between the two authorities.
He said: “Network Rail needs to work in partnership with the city.
“If they fail to do this then we will be less likely to co-operate with them in the future. Building these ramps, in the grand scheme of things for them, is not that expensive.
“I am pretty confident that they will want to do the right thing.”
It is the second council refusal for a bridge of its kind but the first refusal, for the demolition of Hinksey Bridge, was recently overturned by a government inspector.
Under the Oxford and Rugby Railways Act 1845, Network Rail does not have to seek planning permission from Oxford City Council to replace the bridge, but merely needs prior approval.
Prior approval is decided on narrower grounds than normal planning applications.
Decisions hinge on whether the development ought to, or could be reasonably carried out elsewhere, and if the design of the bridge could “injure the amenity of the neighbourhood’’ and be changed to avoid this happening.
The Grandpont footbridge is currently the main pedestrian route for South Oxford residents visiting the 11-acre Hogacre Common eco-park.
Network Rail spokeswoman Anne-Marie Batson said no appeal had been made yet. She said: “We will continue to work closely with the local authority on the planning process as we consider our options.
“However, we are currently funded to replace the bridge like-for-like and unfortunately Grandpoint Bridge is not part of the Government’s Access for All programme for improvements such as ramps.”
Eco-park site manager Ben Hayden said he was in favour of ramped access but that the common was also facing the prospect of losing vehicle access. He said: “If possible we would be keen to have ramp access. But for us that goes hand in hand with vehicle access.’’