"Tomorrow the first plane (with bodies) will leave for Eindhoven" in the southern Netherlands, Rutte told journalists after the bodies arrived in Ukraine's Kharkiv town from rebel-held territory.
"Preparations will be made in Kharkiv so that identification can be done in the Netherlands as well as possible," Rutte said.
"As soon as a victim is identified, first and foremost the family will be informed and no one else. That can take weeks or months."
Rutte said that Organisation for Security and Cooperation in Europe (OSCE) monitors in Ukraine had indicated around 200 bodies were aboard the train, while unconfirmed reports said it contained 282 bodies.
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"As soon as some victims are ready to be transported, the plane will leave," Rutte said, confirming that all the bodies would be brought to the Netherlands and then flown on to their respective countries.
Australia, which lost 37 citizens in the crash, is also sending forensics experts and other investigators to Eindhoven and Ukraine, the defence ministry said in a statement.
Once arrived at Eindhoven, the bodies will be taken to the Kaporaal van Oudheusden military barracks in Hilversum, around 100 kilometres away.
Rutte declined to discuss possible sanctions against Russia, which allegedly supplied the missile that brought down the plane, saying European Union foreign ministers including the Netherlands' Frans Timmermans were currently discussing the matter in Brussels.
He confirmed that the Netherlands would lead the crash investigation, which normally would have fallen to Kiev though it does not control the area around the crash site.
"We will turn over every last stone, and I can tell you that the Netherlands has, at Ukraine's request, been given the lead role in the investigation," he said.