Authorities couldn't say how long it would take to re-open the line, as possible damage to the tracks must first be assessed, but it could take days before services resume.

The cause of Wednesday's incident, which involved a northbound Pacific National freight train derailing and decoupling, before colliding with a V/Line train, remains unclear.

The freight train was reportedly travelling from Melbourne to Griffith.

Heavy machinery, including at least four large cranes, has been taken to the site to clear the wreckage.

Some of the containers are rated to carry up to 35 tonnes.

It may take 18 months for a detailed investigation report to be finalised and released.

The main entry and exit point between the Hume Highway and Barnawartha remained closed on Thursday, with wagons and containers blocking the road.

Other wagons and containers remain pushed up against the passenger train closer towards Chiltern, and at least six containers and two wagons remain tipped further along the line.

Some wagons only derailed by a few centimetres, while others are completely off the track.

IN OTHER NEWS:

Staff from the Australian Rail Track Corporation, Australian Transport Safety Bureau, V/Line and civil companies are working at the scene.

An ARTC spokeswoman said the authority had been unable to conduct a full assessment of the damage.

"The train line currently remains suspended to all services and the site is quarantined for attendance by independent safety regulators and for incident investigations still under way," the spokeswoman said.

"Track opening will be subject to recovery and infrastructure damage assessments following site incident investigations across a roughly 1.7 kilometres long area.

"A more detailed forecast of reopening will be provided once a full assessment of damage to the track is able to take place.

"We will be providing further updates as they become available."

V/Line staff note buses will replace trains between Albury and Melbourne "until further notice".

An ATSB spokesman said "should any safety-critical information be discovered at any time during the investigation, the ATSB will immediately notify stakeholders so appropriate and timely safety action can be taken".

"A final report will be published at the conclusion of the investigation."

There has been at least one other serious incident on the line in the past.

A freight train hit the rear of the Spirit of Progress train at Barnawartha on June 17, 1982, which killed two people on the freight train and injured 20 on the passenger train.

A derailment also occurred at Wodonga on October 23, 2010, when 15 freight train wagons left the track after an axle bearing failed and seized.