Egypt's railway authority (ERA) halted operations from Cairo to Upper Egypt hours after they were resumed Saturday.
According to a statement issued by the ERA, train services have been halted indefinitely due to technical issues in certain destinations between Cairo and Upper Egypt's Aswan, which cannot be fixed immediately.
The ERA has called on passengers to return their tickets for a refund or keep them for future use.
Trains to Upper Egypt initially resumed on Saturday after a 100-day stoppage.
Train services in and out of Cairo were halted mid-August after widespread unrest following the bloody dispersal of two pro-Morsi camps in Cairo and Giza.
In October, 28 services between the capital and the Mediterranean city of Alexandria were resumed.
Under normal conditions, Egypt's railway service transports around 500 million passengers annually, at a rate of 1.4 million per day, according to the Railway Authority's website.