Commuters using the rail line between Chingford and Liverpool Street have faced major disruptions over the last 24 hours.
Yesterday evening, trains were cancelled or delayed after a fault with the signalling system at Bethnal Green.
The same problem occurred on two occasions last week, with trains terminating at Hackney Downs as a result.
The fault continued this morning with operator Greater Anglia telling passengers to seek alternative routes as it was unable to say when the problem will be fixed.
The rail provider tweeted: "#BethnalGreen - Due to the level of disruption it's been advised not to travel unless your journey is essential."
Many people took to Twitter to complain about the service, which affected the majority of trains out of Liverpool Street.
A statement has been released by Greater Anglia this afternoon.
It said: "I would like to apologise for the delays and cancellations that affected our services throughout the morning of Wednesday 18 June.
"This was caused by a signalling problem outside of Liverpool Street, which temporarily prevented us from running many of our scheduled services into the station.
"Whilst we aimed to provide alternative transport arrangements wherever possible, the reduced line capacity on the lines approaching Liverpool Street unfortunately resulted in lengthy delays for many customers.
"We will be investigating the cause of this incident with Network Rail to help avoid any repeat of this problem.
"Customers who chose not to travel may use their tickets on 19 June.
"If your journey was delayed please submit a claim form using our Delay Repay scheme. Details are available from our stations and website."
All lines have now re-opened but some services may be delayed at short notice.