MSP Claire Baker threw up concerns after Network Rail put an official "out-of-use" status tag on the Cameronbridge to Thornton section of the line last week.
She said: "This development is really worrying as it shows that Network Rail doesn't thi
nk the Leven Thornton rail line will be in use anytime soon, even for freight, never mind for the passenger services that we all want to see brought back to Levenmouth.
"Improving transport connections in and out of Levenmouth has to be a priority as better links would bring needed jobs and investment into the area.
"This news will come as a real blow to those that have campaigned for the return of a passenger train service."
However, long-term campaigner Tricia Marwick MSP scoffed at suggestions the rail link was in jeopardy, adding she had been aware of Network Rail's decision for some months.
"Yet again Claire Baker has got it wrong," she said.
"It is true Network Rail has put a temporary stop on the line but the reality is it has not been maintained for years because nobody has been using it.
"This is purely an administrative move."
Mrs Marwick stressed she had been given assurances from Network Rail that if any operator wished to resume operations on the line it would be re-opened within two months.
She added: "I also have a meeting with a minister to discuss this issue as well as the re-opening of the Leven to Thornton link.
"We are still at the same stage as last year when SEStran declared the project was economically viable.
"What we need to do now is keep pressure on the ministers which is what I'm doing."
No freight has been transported on the line since 2001 but Network Rail stated infrastructure would remain in situ.
In a statement the company said it would absorb the costs of returning the line to operational status if an operator requested to use it.
"In this instance, our commitment is to return the branch to an operational standard that would permit two freight trains a day to run as far as the proposed new Diageo facility," the statement read.
The decision would be reviewed in five years.
Ms Baker, however, called on the Scottish Government to step in to get freight on to the line and commit to a future passenger link for Leven.
She said: "It's clear that under this Government, moves to bring a passenger rail link to Leven are going backwards.
"I believe only funding from central Government can bring the return of a passenger rail link to Levenmouth."
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