The Tyne and Wear Metro, which serves Sunderland and Newcastle, apologised to customers online for the disruption.
The faeces was discovered on the train just after 5pm on Saturday at South Hylton station, an operator spokesman said.
A driver closed off the affected carriage before taking the train to South Gosforth station where it was taken out of service.
The incident was revealed after one passenger complained on Twitter about delays and termination of a service on the line linking South Hylton and Airport stations.
In a now deleted tweet the operator replied: “Sorry, the train has been travelling up from Sunderland with only the rear car in operation as someone has defecated on the train and has covered 3 seats with faeces.
“The train has to go into the depot to be cleaned up. Sorry for the inconvenience.”
A spokesman for Nexus, the executive body that runs the Metro, said: “I can confirm that a train was withdrawn from service due to a public hygiene issue in one of the carriages.
“The train was immediately taken back to our depot to be cleaned.
“Incidents like this are rare on the Tyne and Wear Metro but when they do occur the comfort and safety of our customers is our top priority.”
The spokesman said CCTV on the train would be looked at.