On the day where trains returned on the Ballarat line after three weeks of buses, there has already been a number of cancellations and changes for commuters.

The 6.08am service to Ballarat from Melbourne terminated at Bacchus Marsh, with commuters needing to take a bus for the remainder of the journey.

V/Line said this was done because of "scheduled maintenance requirements".

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Then, there were further delays along the line due to a rail equipment faulty near Bacchus Marsh.

The 6.10am Bacchus Marsh service did not run and the 7.10am Bacchus Marsh service will run with a reduced capacity.

Passengers have been quick to vent their frustration at V/Line on Twitter this morning.

"Considering the lines been down for 4 weeks and you guys still can't get first trains running this morning to be on time is crazy and surely embarrassing," wrote one user on Twitter.

"Day 1 after 3 weeks of @vline_ballarat busses. All excited to go on a train... oh wait it's a bus. going to be a long day," wrote another.

V/Line says the problem has been fixed, but there could still be residual delays throughout the morning.