Eastern suburbs rail commuters should brace themselves for more delays on the trip home, with train drivers instructed to go slow and automatic emergency brake triggers switched off.
Metro says that buses will continue to replace trains between Camberwell and Alamein for the rest of the night.
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Problem bat causes headache for Metro
Metro Trains spokesperson Daniel Hoarse says delays continue for the Belgrave and Lilydale lines after yesterday's damage by a bat.
The system will limp along with only one one train at a time able to travel down the lines between Camberwell and Glenferrie stations city-bound, and between Auburn and Glenferrie outbound, until the line problem is solved.
The problem was caused by a bat flying into power lines on Tuesday morning.
Emergency brake systems triggered by stop signals between those stations have been shut off while the problem persists. Instead, platform staff have been forced to "call" through manually to a signal boxes and to drivers.
The go-slow began on Wednesday morning after a letter from Metro Trains general manager of current operations, Wayne Walsh, told drivers to limit their speed to 25 km/h from Camberwell to Glenferrie.
Trains normally travel at more than 70 km/h.
Mr Walsh has told staff to place signals on "stop" and switch trains on ‘‘proceed’’, effectively removing the automatic emergency brake that is triggered when a train passes a stop signal.
Instead of obeying the stop sign, platform staff manually "call" through to a signal box at Burnley and must wait for word from the signal box when each train has cleared the line.
"Only one train is permitted on the down (from the city) line in the section between Glenferrie and Auburn at one time," Mr Walsh wrote.
The letter goes on to say that only one train is allowed on the line between Camberwell and Glenferrie to the city.
A retired driver who contacted Fairfax Media said drivers had contacted him worried about the safety of the operations.
‘‘They are effectively de-commissioning the emergency brake in an effort to get it working at all costs,’’ he said.
Rail, Tram and Bus Union Victoria branch secretary Trevor Dobbyn described the Walsh instructions as "risk mitigation" in line with the rules and operating procedures.
"If it is done to the letter is should be safe," Mr Dobbyn said.
"It slows everything right down. It is a serious response because it is a major fault. They are severe speed restrictions. It keeps it running, trains will be delayed.
"Trains are air-conditioned and it is much better than putting the poor buggers on to buses in 40-degree heat."
Fairfax Media contacted Metro Trains about the letter and risk mitigation and is awaiting a response.
The Alamein line was suspended for most of Wednesday. The Lilydale and Belgrave lines are expected to experience delays of one hour, after re-opening for the evening peak.
February 5 and 6 - long delays on Belgrave, Lilydale and Alamein lines due to signal fault at Camberwell.
January 3 – train derails at Croydon station, causing peak-hour disruption to Lilydale line.
December 21 – Frankston line endure evening peak disruption, with buses replacing trains between Mordialloc and Carrum.
November 30 – Sunbury, Craigieburn, Williamstown and Werribee lines disrupted during evening peak when balloons tangle in overhead power lines at Southern Cross station. Upfield line also disrupted by track fault.
October 29 - signal fault on Sydenham line forces Metro to use buses between Sunshine and Watergardens during evening peak.
August 29 and 30 – fire causes extensive damage to signal cabling on the Frankston line, with buses replacing trains on evening and morning peaks.
June 5 – Sydenham, Craigieburn and Upfield trains forced to bypass the City Loop during the evening peak due to a track fault at Parliament station.
May 6, 2011 – Craigieburn, Sydenham, Werribee, Williamstown and Upfield commuters delayed up to 40 minutes after a signal fault at North Melbourne
November 7, 2008 - Tens of thousands of Oaks Day racegoers stranded when power to the Flemington line fails just as crowds leave the track.
Compiled by Stephen Cauchi