The Queen Street to Anniesland line, via Possilpark and Maryhill, will be the only stretch of track not electrified north of the Clyde in the Greater Glasgow area, leading to transport bosses questioning its viability.
The route was due for electrification as part of the wider Edinburgh Glasgow Improvement Programme (EGIP), but was removed when the Scottish Government amended the scheme to cut costs.
The line runs from Queen Street, with stations at Ashfield, Possilpark & Parkhouse, Maryhill, Gilshochill, Summerston and Kelvindale, and was only completed in 2005 as part of a £35 million project. It joins the main intercity route near Cowlairs junction.
The line was threatened under the original EGIP plan to allow extra services to operate in and out of Queen Street Station.
However, following pressure from local politicians and the Evening Times Save Our Stations campaign, assurances were given that the line would remain open, and when the additional services were removed from EGIP it appeared to be safe.
But transport bosses fear the latest proposals leave the line isolated and vulnerable.
A report for SPT councillors to be considered this week states: "The revised proposals now raise a more serious concerns on the future of this line, as is has been excluded from any electrification.
"This line would be the only section of non-electrified route north of the Clyde in the SPT network and therefore have limitations as to the type of rolling stock, performance of the line and hence major effect on patronage."
SPT is raising the concerns with Transport Scotland and asking for the line to be electrified to guarantee its future.
It is also suggested the line be connected to the North Clyde line, which would mean services wouldn't terminate at Anniesland and passengers could be able to continue to Hyndland and Partick without changing trains.
Jim Coleman, SPT chairman said: "SPT supports the electrification of Scotland's railways but these latest plans don't stack up.
"The proposals will disadvantage many local networks vital to our economy and we don't yet know the true cost of the changes, nor do we have full detail on how disruption to services will be managed.
"The exclusion of the Maryhill line from electrification could potentially isolate that area from the rest of the network.
"I am very concerned about the future of that route and the passengers who depend on it."
Politicians who campaigned to save the line last year were concerned that it may be at risk once again.
Patricia Ferguson, MSP for Maryhill and Springburn, raised questions when it was previously discovered the EGIP works would mean the line could be closed off at the city end, adding 30 minutes to the journey time.
She said: "This is extremely worrying. We had reassurances from the minister about the future of the line.
"The current proposals seem to throw that into question.
"I will be seeking urgent meeting with the minister.
"This is a well used line with growing numbers of passengers."
Local people spoke out against the previous threat of closure and Glasgow City Council leader Gordon Matheson opposed closure.
Last year he was given an assurance from Transport Minister Keith Brown that services in the north of the city would not be damaged by the EGIP plan.
A plan to revamp Queen Street station as part of a £650 million project to electrify the Glasgow to Edinburgh rail line has also been questioned by city transport bosses.
SPT believe that with High Speed Rail plans only seven years behind the EGIP completion, then a full scale station redevelopment is unnecessary.
The initial EGIP plan would have seen more trains running on the line with an increased frequency between Queen Street and
When that was
abandoned, and the programme costs slashed from £1.2 billion to £650m, the plan was to run fewer but longer trains.
To accommodate eight carriage trains it is proposed to lengthen the platforms at the station, meaning extending out into the concourse area
and extending the
station towards George Square.
There are concerns that with plans for more shops in the station there will be less room for passengers and the concourse will be even more congested at busy times that at present.
SPT said that one platform can already take eight carriages and the others can take seven, which would
reduce overcrowding at peak times.
In a report to councillors SPT assistant chief executive, Eric Stewart, said: "The inclusion of a whole scale redevelopment of Queen Street Station would be questionable if High Speed Rail were to come into place only seven years after the redevelopment."
Jim Coleman, SPT chairman, said: "I see no logic to the planned overhaul of Queen Street and how this will fit with a longer term commitment to a high speed rail network.
"The level of chaos this will cause just a few years before further big changes are potentially necessary just doesn't make sense."
A Transport Scotland spokesman said: "The redevelopment of Queen Street will transform the passenger experience, enabling existing platforms to be extended to accommodate longer trains.
"The improvements are essential to meet passenger demand on the Edinburgh/Glasgow via Falkirk High route, which we expect to exceed available capacity by the end of this decade. Including the redevelopment of Queen Street will future proof capacity on this critical route.
"High Speed rail is a longer term objective and, when introduced, will add to the opportunities for travel between Edinburgh and Glasgow and meet future passenger growth."