In November and December, the main line at Cowley Bridge near Exeter was submerged, closing it for 11 days.
Business leaders and Devon and Cornwall's councils have written to the Environment Agency and Network Rail.
Network Rail has insisted work is being done to improve the situation.
The joint letter said that while the "severe impact" the closure of Cowley Bridge had on Devon and Cornwall's economies had been recognised, there was still "no firm, positive and long-term solution".
Network Rail said a bid for £30m had been submitted to the government which would pay for work at 10 locations to make the South West's rail tracks more resilient against flooding and landslips.
But the letter said although work was due to be carried out in January, it did not include work at Cowley Bridge.
The letter concluded by asking for confirmation from Network Rail and the Environment Agency that a solution  "acceptable to the region as a whole" to stop flooding at Cowley Bridge was found as soon as possible.
Mike Gallop, Network Rail's route asset management director, said a detailed study had been carried out after the flooding.
"I think it's very important to state that we're not proposing to stop the flooding at Cowley Bridge," he told BBC News.
"What we are proposing is to improve the resilience of the railway - to recover the service and recover the track and signalling much more effectively than we did last year."
Mr Gallop said Network Rail fully recognised the importance of rail services to the South West economy and a looking for a solution was a priority.
"The railway to the South West is a priority - not only Cowley Bridge," he added.
Concerns have been raised that not enough is being done to prevent a repeat of serious flooding which disrupted rail services in the South West last winter.