Technicians are at the scene, attempting to solve the problem, and a rescue train is en route to assist the break down.
The routes affected are the CrossCountry train between Birmingham New Street and Stansted Airport, and the Greater Anglia services between Kings Lynn and London Liverpool Street, and between Norwich and Stansted Airport.
Trainline, an independent digital rail and coach ticketing platform, released information regarding the issues: "A broken down train at Audley End is causing disruption to journeys between Cambridge and Stansted Airport/Bishops Stortford. As a result of this, trains may be cancelled or revised.
"This is expected until 6pm."
CrossCountry services between Cambridge and Stansted Airport have been cancelled.
People intending to travel on the Greater Anglia routes were advised to use their tickets on Great Northern services between Cambridge and London Kings Cross and on London Underground between London Kings Cross and London Liverpool Street.
A Greater Anglia spokesperson said: "We're very sorry for the disruption and delays caused to customers after one of our trains broke down at Audley End station this afternoon. Customers on board were able to complete their journey to Stansted, although partly by taxi.
"The broken-down train is blocking the line, so we are currently advising customers not to travel between Cambridge and Bishops Stortford/Stansted Airport.
"We sincerely apologise for the inconvenience this causes to customers. Anyone who has been delayed by 15 minutes or more should contact Greater Anglia about delay repay compensation."
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