V/LINE was scrambling to deal with a backlog on the Ballarat line yesterday, after an early-morning train struck a tree near Gordon.
The 5.31am Wendouree to Southern Cross service clipped the tree which had fallen from private property onto the tracks overnight.
All 80 passengers waited on the tracks for several hours as emergency repairs were carried out on the train.
V/Line spokesman James Kelly said due to the isolated area where the collision occurred, bussing passengers away was not an option.
Instead, V/Line crews performed temporary repairs and towed the stricken train and five carriages back to Ballarat.
All morning services following the accident were switched to road coaches.
Mr Kelly said the distance from the train to any roads or access points made it inappropriate to remove the passengers from the train.
He said the train suffered damage to some of its air hoses, which meant the train's brakes locked in place until repairs were made.
"The passengers were due to get into Melbourne at 6.55am, but they arrived just after 11am," Mr Kelly said.
"We had enough road coaches to cover the other services affected."
V/Line passenger on a later train, Anthony Pawczynski, said he often travelled from Melbourne to Ballarat for work.
He said he understood that the delays yesterday were not the fault of V/Line.
"What do you do? It's been windy, tree roots get loose and that's what happens," Mr Pawczynski said.
"I'm not frustrated but it's inconvenient."
Fellow passenger Rani Hansen agreed.
"I don't need to be in the office until 10.30am so for me, I'm a lucky one."