Rail workers have said their health is at risk because they are being sprayed with human waste from passing trains.
The Rail Maritime and Transport union said excrement on board GNER trains is being released on to tracks when they travel at speed or brake heavily.
The problem was raised by workers in Darlington and at the North East depot in Heaton, Newcastle, 18 months ago.
GNER said it had carried out an investigation and was spending £500,000 on a new tank emptying facility.
Bob Crow, general secretary of the RMT, said the train company was flouting safety rules.
He said: "GNER have finally admitted that they have known for years that their trains are spraying human excrement into the atmosphere but they have yet to stop it happening.
"At one point it was suggested that track workers simply turn their backs when one of these trains approached, but not only would that not stop anyone breathing in the spray, it is completely contrary to safety rules."
A GNER spokesman said the problem related to a lack of tank emptying facilities at the Heaton depot.
He said: "The problem related to a lack of tank emptying facilities at the Heaton depot, run by Northern Rail. Heaton is one of six depots used to stable GNER trains overnight.
"All of the other depots we use have dedicated tank emptying facilities which allow retention tanks to be routinely emptied nightly as normal procedure.
"A temporary tank drainage facility was introduced at Heaton, and the frequency of tank emptying increased.
"GNER, in partnership with Network Rail and Northern Rail, are installing a permanent tank emptying facility at Heaton at a cost of more than £500,000."
He also said there was no risk to the health of passengers and that track workers had been given hygiene advice.