A deal between unions and the Scottish Government scrapped the practice by December 2017 but a shake-up in the ScotRail fleet will lead to its return.
RMT boss Mick Cash said a senior ScotRail staff member has confirmed of the 10 high-speed trains expected to be in service by December, only one will be fitted with a tank for human waste.
He has written to the company’s managing director Alex Hynes and Transport Secretary Michael Matheson calling for urgent action on the issue and highlighting the “serious health risks” posed.
Prior to the agreement coming into force the trains had toilets which discharged waste onto the tracks, which were then upgraded with Scottish Government funding.
ScotRail is bringing in a fleet of 26 refurbished high speed trains but in a programme which has faced several delays.
Not all of the trains have been refurbished but, to prevent cancellation of services, the unrefurbished models - which empty waste onto the tracks - will be brought in to prevent gaps.
A rolling programme of refurbishing the trains will continue, with Transport Scotland saying all would have tanks fitted by next year, but in the meantime the waste agreement will be breached.
RMT General Secretary Mick Cash said: “Our members are rightly appalled that Scotrail have sought to rip-up a clear agreement to end the filthy and disgusting practice of dumping human excrement on Scotland’s railways.
“This disgraceful and retrograde step must be halted now and the union will take whatever action is required to hold ScotRail to their agreement with the union.
“One minute ScotRail are bragging about their aim to operate the most modern railway in the world and the next they are back to spraying track workers with human waste.”
A ScotRail spokesperson said: “The first of our upgraded Inter7City high-speed trains has entered service, and has received very positive feedback from our customers.
“We are working flat out to get more upgraded trains into service as quickly as possible, but our supplier, Wabtec, is behind schedule and has let us down.
“To ensure we can deliver services for our customers we will introduce classic high-speed trains until enough upgraded Inter7City trains are available. These classic trains will not have retention tanks, which is far from ideal. We are doing everything we can to mitigate this as soon as possible.”
A Transport Scotland spokeswoman said: “We understand this interim measure is regrettable, but necessary to support more services and jobs across the country while retaining passenger services between our key seven cities.”
She added Transport Scotland sympathises with the unions and would prefer to have all the refurbished trains in service, saying the company carrying this out must deliver on their work as soon as possible.