In 2017, Network Rail agreed with the government to stop the practice of dumping sewage onto the rails by the end of 2019.
However, due to delays in upgrading its train fleet, Northern is among a number of operators which will fail to meet this target.
A spokesman for the beleaguered operator, which runs the majority of trains through Bolton, said Northern was in the process of dealing with the issue.
“Our existing fleet of 243 trains is undergoing a complete refurbishment and as part of this programme, we are updating a number of our older trains which currently do not have waste retention tanks," they said.
“Whilst this is an industry wide issue, we are working hard to improve the railway environment for customers and railway workers.
"Based on our upgrade programme, we expect 100% of our trains to be fitted with waste retention tanks by the middle of next year.”
Older trains have to be upgraded with new tanks in order to hold enough waste so as not to have to dump.
The issue is of particular concern for railway workers, who sometimes have to stand trackside while passing trains dump their unsavoury loads.
In response to questions about dumping waste, a spokesman for Network Rail said: “We are committed to putting an end to trains emptying waste onto the tracks and we are working with all operators to make this happen. There are a few train companies that have been given a bit more time for a small number of their trains and we are tracking their action plans closely to make sure they comply.”