The packed bodies were loaded into wagons at a station in the town of Torez, some 15 kilometres from the crash site, and the train left for the rebel-held Ukrainian city of Donetsk, Ria Novosti news agency reported.
The smell at the station was unbearable and separatists guarding the grisly cargo had pledged not to move the bodies until "international experts" arrive, Organisation for Security and Cooperation in Europe (OSCE) spokesman Michael Bociurkiw said.
There are a total of 198 bodies on the train, according to OSCE monitors who inspected the train ahead of the departure. Armed rebels were guarding the train.
OSCE monitors escorted by armed rebels appeared today to have been granted greater freedom to examine the crash site.
The Malaysia Airlines Boeing 777 carrying 298 people was flying from Amsterdam to Kuala Lumpur as it was downed on Thursday between Krasni Luch in Luhansk region and Shakhtarsk in the neighbouring region of Donetsk.
The Ukrainian government and pro-Moscow rebels have been trading blame for the downing of the airliner.
Western countries have criticised the pro-Russian rebels in the area for restricting access to the crash site.
Indiscipline and chaos ruled at the crash site in the last two days.
The US State Department said there had been multiple reports of bodies and aircraft parts being removed, and potential evidence tampered with.
Meanwhile, France warned Russia of "consequences" at the EU if Moscow did not "immediately take the necessary measures", after the leaders of France, Germany and Britain held a conference call.
Raising the prospect of fresh EU sanctions against Russia over the downing of the Malaysian jet, British Prime Minister David Cameron, in an article in The Sunday Times, said the West must "fundamentally change our approach" unless Moscow alters course in Ukraine.
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