About 40 coffins were laid out at the airport in the government-held city of Kharkiv on Wednesday morning in preparation for the flight.
A refrigerated train carriage carrying about 200 bodies arrived in the city on Tuesday, four days after the crash.
As the bodies departed Kharkiv airport, Pastor Vitaliy Sorokun from the city's New Hope Church told Premier's 'News Hour' that local people have been praying for the victims, he said: "they went to the main square and they actually hanged the flags of every nation which lost the lives of these precious civilians on the jet ."
A total of 200 bodies have so far been accounted for from the 298 victims, 193 were Dutch nationals.
The king, queen and prime minister of the Netherlands will lead mourners as the first victims of the Malaysia Airlines disaster are repatriated from Ukraine today to the town of Eindhoven on military aircraft.
It's thought their identification could take months.
Professor of medical forensics Peter Vanezis thinks experts will have to rely on information provided by the families, he said: "They will be able to look at dental records. They will also be able to test for DNA; in some cases fingerprints or any other medical implants or anything like that that are present on the bodies."
The black boxes from the downed Malaysian plane have been delivered to the Air Accidents Investigation Branch [AAIB] headquarters at Farnborough in Hampshire.
The AAIB has said it will take 24 hours to download the data from each machine.
Meanwhile, America's blaming Russia for "creating the conditions" that led to the Malaysia Airlines plane crash.
But senior US intelligence officials admit there's no link between Russia and the missile which reportedly brought the plane down in eastern Ukraine.
Instead they suggest pro-Russian separatists shot it by mistake.
Prime Minister David Cameron also believes Russia could be helping air crash investigators, he said: "the people who probably have the really valuable information about what happened to this flight are indeed the Russians themselves and they should release what they know about what happened"
Meanwhile, the Ukrainian military says two fighter jets have been shot down by pro-Russian separatists in the east of the country.
Fighting is continuing in the region , with heavy fighting in Luhansk and villages near the scene of the crash.
Elsewhere, a charity appeal set up by a victim of flight MH17 has broken through the £10,000 barrier.
20-year-old Richard Mayne set up a JustGiving page in January for the Kidasha charity, which helps families living in poverty in Nepal.
The student travelled to the country for voluntary work in March.
London-based Kidasha say their hearts go out to all Richard's family and friends and they're very grateful for the donations.
Pastor Vitaliy Sorokun from Kharkiv's New Hope Church: