V/Line has confirmed a track fault between Sunbury and Bendigo impacted five morning services on the Bendigo line.
Services in both directions were affected.
The fault was rectified at 8.20am but some residual delays continued.
"We apologise to passengers on the Bendigo line who experienced delays this morning following a track fault," a V/Line spokesperson said.
"We understand the frustration service delays cause, and our team worked to fix the fault as quickly as possible."
Passengers who were delayed for 60 minutes or more could be eligible for compensation.
V/Line has encouraged passengers to call 1800 800 007 to check their eligibility.
The Bendigo V/Line 6.16 service from Southern Cross is now expected to be delayed for approximately 45 minutes.
The Bendigo V/Line 6.16 service from Southern Cross has been delayed for 20 minutes.
V/Line has tweeted that a rail equipment fault is to blame.
The 7.23 Kyneton to South Cross Station service has also been delayed by approximately 40 minutes due to the equipment fault.
There has been no information as to whether other services will be affected.
It follows services on the Ballarat line being delayed up to 70 minutes on Monday.
V/Line said an operational incident involving a signal near Rockbank was the cause.
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