Australian officials will observe as the remains of their compatriots are loaded onto a Netherlands military transport plane and flown to Amsterdam for identification.

The bodies will then be returned to their home cities, and their grieving families.

Separatist leader Alexander Borodai, who describes himself as prime minister of the Donetsk People's Republic, said early on Tuesday morning that the train had come into Donetsk, en route to Kharkiv.

It was unclear whether the train had then continued on from Donetsk.

Video shot previously by journalists in the area showed heavy damage to a train line to the north of Donetsk, however there was more than one route the train could take from Torez to Kharkiv, Ukraine authorities said earlier.

"We are looking at four routes, considering four routes, for us there is no big difference which route it will go," vice prime minister Volodymyr Groysman told reporters.

The most important thing was that the train start moving, he said.

Meanwhile, Australian flight crash investigators are preparing to head to the crash site to begin investigating the cause of the tragedy, as part of an international team led by the Dutch.

At 7pm on Monday evening, local time in the eastern Ukraine town of Tolez near the MH17 crash site, two trains left the station pulling refrigerated carriages, containing 282 bodies and 87 fragments of bodies from the Boeing 777 that fell from the sky last Thursday.

While it cannot be certain until forensic work is finished - and the search of the crash zone continues - officials believe those body fragments comprise all of the other 16 people on board the flight.

The trains – which waited more than 24 hours for clearance to travel - were to make their way through separatist-held territory, with the rebels’ permission, and head for the northern Ukraine city of Kharkiv, which contains the country’s second international airport.

Three members of a Dutch forensics team, and six Malaysian representatives were to ride on the trains.

As soon as the trains reach Kharkiv the bodies were to be transferred to trucks and taken to the airport.

The bodies will pass through a security scan and be put on a Dutch military aircraft waiting to take them to the Netherlands.

Once there, the bodies will be examined and identified at a state-of-the-art forensics laboratory.

Several Australian consular officials – who travelled to Kharkiv from Kiev by train on Sunday night - will accompany the flight, and around 20 Australian forensic experts will assist with the Dutch forensics team, as well as Malaysian experts.

The transfer of the bodies from the trains to the plane will be observed by Australia’s ambassador to Ukraine, Jean Dunn, along with a defence attaché flown down from London.

On arrival in the Netherlands the plane was due to be met by Neil Mules, Australia’s ambassador there, and another defence attaché, who will help oversee the work.

DNA samples and dental records will be used to identify the bodies. When the forensic work is complete the Australian bodies will be sent home, most likely in temporary coffins on an Australian military plane.

Ukraine Vice Prime Minister Volodymyr Groysman, head of his government’s MH17 taskforce, said Ukraine had pushed through the official documentation to allow the bodies to leave the country.

While human forensic work concentrates in the Netherlands, Australia also has contributed members to an international team investigating the cause of the crash.

Some are already in Ukraine and more are due to arrive in coming days.

Australian representatives have met with officials in Ukraine, including the OSCE group of international observers, to arrange getting the team to the crash site.

However, plans have not yet been settled, at time of writing – and Australian officials are concerned by the shelling of Donetsk, and its consequences for the safety of their people.

Fairfax understands that Ukraine’s military offensive on Donetsk on Monday may have added to the uncertainty and delay over the trains’ departure from Tolez.

On Monday evening the Ukraine government committed to taking no military action within 40km of the crash site, in order to help the investigation.

And the government and president have pledged full co-operation with, and assistance for Australia’s work in Ukraine.

However, it did not agree to a ceasefire in other surrounding areas, as it continues to try to take back territory from the pro-Russia separatists.

The Dutch are leading the crash investigation, at the head of a team comprising experts from around the world.

Some were already on site on Monday, taking photographs of the plane wreckage – which has been picked over and looted over the last four days.

An international official close to the investigation told Fairfax that it appeared the integrity of the crash site had been completely undermined.

The usual first step in a crash investigation is to secure the entire site from interference.

Ukraine has accused the Russian secret service of trying to wipe the site clean of evidence that the plane had been hit by a separatist forces’ missile.

A small number of Australian relatives have asked to visit the crash site, Fairfax understands, however, it does not appear feasible in the near future due to military action nearby.