A passenger train passed through two level crossings on Tuesday and the boom gates failed to lower in time.

The safety breach occurred while the locomotive-hauled train was travelling between Camperdown and Terang.

Trains will be suspended for at least the next four days, possibly longer, forcing passengers travelling to and from the state's south-west coast onto buses.

On Tuesday evening, V/Line's website also listed "major disruptions" on the Geelong, Ballarat and Bendigo lines.

A V/Line spokeswoman said the delays were due to a train fault at Footscray Station.

"V/Line engineers worked to repair the fault on the train, which was unable to move and was blocking the path of other services," she said.

The spokeswoman said there were delays of about 60 minutes at 8pm.

Meanwhile, the same level crossing failure occurred at a crossing north of Bendigo this week, prompting V/Line to quietly shut down the Echuca line on Tuesday and replace all trains with coaches.

The incidents again call into question the safety of the V/Line rail network, which has experienced multiple level crossing failures of this type, including on the Traralgon line in January.

That incident prompted Metro to ban all V/Line trains from using metropolitan rail lines until the issue was fixed.

Boom gate failures have also caused extended shutdowns of the Bairnsdale and Stony Point lines in recent years, forcing costly rectification work before trains could return to service.

V/Line spokesman Rob Curtain said Warrnambool trains were suspended after warning bells and booms failed to lower in time.

"The replacement services are the result of a recent incident at a level crossing on the Warrnambool line in which lights, bells and boom gates activated at a level crossing with a warning of 20 seconds instead of 25 seconds as designed," Mr Curtain said.

On the Echuca line, the booms lowered just 16 seconds before the train approached, nine seconds later than they should have.

V/Line informed Jacinta Allan, the public transport minister, early this week of the boom gate failure that shut down the Echuca line for three days.

Mr Curtain said there was no danger to passengers, V/Line staff or road users.

Motion detectors to activate the crossings were being adjusted to provide the maximum warning, regardless of train speed, he said. 

Trains to Echuca were expected to resume later on Thursday.   

Level crossing safety fears are also behind a string of heavy speed restrictions that have been slapped on trains between Geelong and Warrnambool since October 12.

As of this week there were 29 country crossings on the line where train drivers have been instructed to slow down, to as low as 40km/h in the worst cases.

This is due to "inadequate sighting distance" and "line of sight problems" at the affected crossings.

Warrnambool line trains ordinarily run at speeds of up to 115km/h, however concerns among train drivers about poor track condition led to this being reduced to 100 km/h.

Track faults and safety concerns at rural level crossings have played havoc with Warrnambool line services in recent weeks and passengers have endured chronic late-running trains before this latest incident.

Just 61 per cent of trains ran on time in October, easily the worst performance of any V/Line rail line in recent months, marking a return to poor service levels not seen since summer when V/Line suffered a severe train shortage caused by unexpected wheel wear problems.

The wheel wear, which only affected VLocity​ trains, plunged V/Line into meltdown on most of its busiest lines, and led to the resignation of its chief executive Theo Taifalos​ under intense political pressure from the Andrews government.

The Opposition called on the government to clarify whether locomotive-hauled trains would be suspended from other lines they service as a safety precaution, with public transport spokesman David Hodgett saying "level crossing safety should be a given".

"Daniel Andrews and Jacinta Allan need to urgently explain whether all V/Line long distance locomotive hauled trains to Warrnambool, Albury, Bairnsdale and Swan Hill will be immediately withdrawn, what the cause of this potentially very dangerous incidents was and why Mr Andrews and Ms Allan have stayed silent," Mr Hodgett said.

It is not the first safety problem on the Warrnambool line this year.

A V/Line train carrying almost 100 passengers collided with a truck at the unprotected Phalps Road level crossing in July, which had been earmarked for an upgrade. No one was killed but the truck driver, the train driver, a conductor and 16 passengers were injured in the smash.