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Monitors from the Organisation for Security and Cooperation in Europe, accompanied by armed rebels, checked the wagons. A locomotive had been put at the head of the train, which one worker said would be sent southwest to an undisclosed location.
Western officials have voiced concern about the handling of the remains of the 298 people killed when the airliner crashed on Thursday and the Dutch foreign minister has said his country is "furious" to hear bodies were being "dragged around".
After lying there for two days in the summer heat, by Sunday the bodies had been removed from a large swathe of the crash site, leaving only bloodstained military stretchers along the side of the road.
Sergei Kavtaradze, a senior official of the pro-Russian rebels' self-proclaimed Donetsk People's republic, said all 196 of the bodies found so far had been loaded into the wagons in Torez, an eastern town in the Donetsk region.
"They will stay there for now, until the issue (of what to do with them) is resolved. We are waiting for the experts," he told Reuters, saying he did not understand why the experts had been delayed.
"We've been waiting for the experts for three days. From the very first day after this catastrophe, we have welcomed any experts. Ukrainian experts, international experts, Russian experts... We have always said we will offer the maximum guarantee of their safety in the territory we control."
Alexander Hug, deputy chief monitor of the OSCE special monitoring mission to Ukraine, said his team had seen body bags in the wagons but were unable to count them. He said he did not know where the bodies would be taken.
One railway worker said the bodies were brought in during the night and would be sent in the direction of the town of Ilovaisk, southwest from Torez.
"Something was delivered and they told us to wait," one railway worker said on condition of anonymity, adding that the "something" were bodies.
"It's corpses. They brought the bodies overnight," a duty officer at the Torez station told Reuters.