The loading of four of the coffins, chosen symbolically, on to a Dutch Hercules military transport aircraft signalled the start of an operation that is likely to take days to complete.

But after assurances in recent days that virtually all passengers and crew on the Malaysia Airlines Boeing 777 had been accounted for, the Dutch leader of the investigation revealed late on Tuesday that as few as 200 bodies had been packed into the four refrigerated rail wagons that delivered them to Kharkiv on Tuesday.

On the tarmac at Kharkiv airport on Wednesday morning dignitaries from the countries of the victims and the military services of Ukraine formed a guard of honour as the first coffins were placed on the aircraft.

A prominent Australian symbol in the crowd was the Diggers' slouch hat worn by Colonel Peter Steel, military attache to the Australian ambassador in Kiev, Jean Dunn, who also attended the ceremony.

Speaking on behalf of Prime Minister Tony Abbott, special envoy Angus Houston said: "We are here as representatives of many nations to honour and to pay respect as their journey home begins – we are united in grief but we are determined to give them respect and dignity for their journey. This has been a tragedy of unspeakable proportions," he said in his slow deliberate Australian accent.

The Houston reference to dignity and respect was an oblique reference to a painstaking process that has begun in an old Soviet-era munitions factory in Kharkiv, with each of the body bags delivered from the crash scene being packed into a second body bag and then being placed in simple timber coffins for the journey to the Netherlands, where the detailed process of identification will begin.

The grim reality of the contents of the four Soviet-era chilled wagons that lumbered here from Torez, a community 15 kilometres from the crash scene, casts global criticism of the conduct of the search and recovery in the fields of eastern Ukraine in a disturbing new light. It also utterly undermines the credibility of the Kiev government, which on Monday had given assurances that virtually all the passengers and crew had been accounted for.

Mr Abbott's suggestion that international forces should take control of the crash scene will likely get serious consideration and support with the realisation that a huge new phase of the search for human remains is required given the new uncertainty that the remains of all of the 38 Australians on board the Malaysia Airways flight from Amsterdam to Kuala Lumpur have been recovered.

A decision on Monday by the separatist rebels who control the crash scene to release the bodies and to hand over the black box flight data recorders was expected to ease rising international anger and consternation at the conduct of the crash investigation to date.

Anger has centred on bodies being left in the humid summer heat for up to three days, and now for much longer given that 100 remain missing; the looting of baggage; and the failure to secure the scene, to protect evidence that will be vital for what will be a protracted investigation.

Also infuriating for the governments of the victims was the refusal by the separatists to give investigators free access to the site, which in places has been trampled as well-meaning locals conducted a less-than-professional search.

There were signs of renewed anger and resolve when the Dutch official Jan Tuinder became adamant, saying of those still missing: "They will be found. I know that we do have to go back to sweep the [crash] area.

“It's an enormous area, we all know that. It's more than 14 kilometres in length, but we will not leave until every remains has left this country, so we will have to go on and bargain again with the people over there.”

For now, he said, the priority was to return the bodies from the train to their home countries.

Pressed for two days running by Fairfax Media on Mr Abbott's suggestion that an international force be sent to secure the crash scene, Ukrainian Deputy Prime Minister Volodymyr Groysman refused to state his government's position saying only that his government was eager to work within Ukrainian and international law and to work under any agreements approved by his country's high officials.

He told the gathering, "I'm not sure if the people who filed the missile know anything about dignity or the value of human life, but their punishment awaits them."

The Netherlands has declared Wednesday a national day of mourning for the 193 Dutch victims of the crash, with the first aircraft scheduled to arrive in the country in the late afternoon.

King Willem-Alexander and Queen Maxima are to lead what inevitably will be an emotional reception of families and friends at Eindhoven Airport.

Dutch government spokeswoman Ester Naber told Fairfax Media that despite earlier predictions of a speedy processing of the bodies it likely would take days before all had been airlifted to the Netherlands, she said: people think it's a simple process, but it's very difficult. we have professionals working in complete forensic bodysuits and they have to proceed with the utmost respect and accuracy and that takes time."

Asked to clarify the new Dutch estimate of only 200 bodies having only been delivered to Kharkiv she said: "Look, we have at least 200 - but we won't know how many until we have opened all the bags. There could be bags containing parts that belong to several people, we think we have at least 200 but we don't know. What we do is it's significantly less than 282."

After the ceremony Mr Houston said that Canberra was responding cautiously to the Dutch assessment that as few as 200 bodies had been recovered.

"I don't think we know how many bodies until we have been through the full identification process. When an aircraft comes down from 33,000 ft the human body is subjected to incredible trauma.