A train which derailed on Thursday night, leaving two drivers dead and 11 passengers injured, will be winched off the tracks at Wallan on Sunday.

Investigators says they have now completed an on-site probe into the tragedy, with some of the locomotive units and passenger carriages to be removed from the area using heavy machinery, before they are relocated for more damage assessments.

A number of functional carriages will be placed back on the tracks and connected to the locomotive unit at the back of the train, which was undamaged, before being transported by rail.

The XPT train derailed at Wallan on Thursday night. CREDIT:AAP

The Sydney to Melbourne XPT service was carrying 153 passengers at the time it came off the tracks around 500 metres away from the Wallan train station.

John Kennedy, a 54-year-old XPT driver from the ACT, and the train's pilot, a 49-year-old from Castlemaine, died in Thursday night's derailment.

Crews have been sent from Sydney to assess whether segments of the train could be reused, such as the diesel locomotive unit at the rear of the XPT which remained on the tracks.

A media spokesperson for Transport NSW said the current level of damage to the train was unknown and, once preliminary assessments are completed, the train will be transported back to New South Wales.

"The process is going to take a number of days, it does depend on a number of factors ... access to the site is quite difficult," the media spokesman said.

The Australian Transport Safety Bureau (ATSB) have completed "the majority of their on-site evidence collection work" at the site as of Saturday, a media spokesman confirmed.

"The ATSB released the track back to the infrastructure manager, ARTC, on Friday evening, and the rolling stock back to the train owner, Sydney Trains, on Saturday morning," the ATSB spokesman said.