Aslef will next week debate a motion at its annual conference in Edinburgh calling for such “floral shrines” to be taken down because of drivers’ distress.
The union said such unofficial memorials, which have also included scarves and soft toys, normally appeared after every death and on anniversaries.
About 24 people a year are killed on Scotland’s railways, most of them suicides. Many train drivers witness such incidents and some leave their job as a result.
Aslef said many such tributes had been cleared away, but those remaining included at Holytown in North Lanarkshire and near Inverurie in Aberdeenshire.
At Holytown, it said a “huge amount” of flowers on a footbridge had blown over the track, while a large teddy bear had been tied to railings.
Aslef Scottish district secretary Kevin Lindsay said: “These floral tributes are a reminder of fatalities on the railway and often drivers endure flashbacks to other fatalities.
“No-one wishes to come to work and be reminded that someone has died there.
“Often drivers suffer extreme reactions to fatalities and never return to driving.
“As a union, we respect the right of families to mourn and believe Network Rail should have a memorial at a major station which families can use as a focal point for their grief.”
Aslef said other sites included Milliken Park station in Renfrewshire, where deaths have included a couple who were taking a shortcut across the line.
It said: “This was particularly bad, with the sheer amount of floral tributes. It upset a lot of drivers.”
The union said at Edinburgh Park station, a driver had to slow to 5mph because dozens of mourners grouped round a shrine holding candles and flowers were standing close to the edge of the platform.
The Samaritans, which is drawing up guidance “strongly” discouraging such memorials, said they could increase suicidal behaviour.
The draft guidance said: “Public memorials illustrate an outpouring of grief and expression of regret. Normalising or sensationalising a suicide can act as a catalyst to influence vulnerable people to copy.”
It also said memorials “can label that location as a hotspot, drawing other suicidal individuals to it, or highlighting it as a suitable location to achieve a completed suicide.
“Train drivers who experience a fatality by suicide can often suffer from varying levels of post traumatic stress.
“Once back at work, they often will drive the same route, and seeing memorials line-side or at stations becomes a daily reminder of the event. This can induce greater level of trauma and exacerbate distress to the driver.”
Inverurie councillor Martin Kitts-Hayes, where two people have died this year on the rail line, said: “I can see it from both sides - I can well understand families wanting to pay tribute, but for drivers it is a constant reminder of what happened.”
A ScotRail spokeswoman said: “Floral tributes can bring comfort to families and friends, but we are also aware of the impact they can have on our staff.
“We aim to deal with these tragic situations individually, in a sensitive manner, and in a way that respects the wishes of all involved.” We would be happy to discuss this further with union representatives.”
A Network Rail spokesman said: “Any incident has to be considered on its individual circumstances and due consideration given to the needs of relatives, passengers and staff. Floral tributes are only removed from Network Rail land after a suitable period of time has passed.”