The train carrying around 200 body bags arrived in the eastern city of Kharkiv, which is in Ukrainian government hands. The bodies will then be taken back to the Netherlands to be identified.
Members of the media take pictures of black boxes belonging to Malaysia Airlines flight MH17, before their handover from Ukrainian pro-Russian separatist to Malaysian representatives, in Donetsk. Reuters
Read: Russia says MH17 probe should be done by 'international community', not Ukraine
The train left the crash site after the Malaysian prime minister agreed with the separatists for recovered bodies to be handed over to authorities in the Netherlands, where two thirds of the victims came from. Read full coverage
The handover and reports by international investigators of improved access to the wreckage of the airliner four days after it was shot down, came amid calls for broader sanctions against Russia for its support for the rebellion, although Western leaders are struggling to agree on a response.
Early on Tuesday, senior separatist leader Aleksander Borodai handed over the black boxes in the city of Donetsk.
"Here they are, the black boxes," Borodai told journalists at the headquarters of his self-proclaimed Donetsk People's Republic as an armed rebel placed the boxes on a desk.
Colonel Mohamed Sakri of the Malaysian National Security Council said the two black boxes were "in good condition".
Watch: MH17 crash: Black Boxes of downed jetliner turned over
Shaken by the deaths of 298 people from around the world,Western governments have threatened Russia with stifferpenalties for what they say is its backing of pro-Russianmilitia who, their evidence suggests, shot the plane down.
At the United Nations, the Security Council unanimously adopted a resolution demanding those responsible "be held toaccount and that all states cooperate fully with efforts toestablish accountability".
It also demanded that armed groups allow "safe, secure, fulland unrestricted access" to the crash site.
"We owe it to the victims and their families to determine what happened and who was responsible," said Australian Foreign Minister Julie Bishop. Australia lost 28 citizens in the crash.
The Kremlin said on Monday that President Vladimir Putin spoke to Dutch Prime Minister Mark Rutte by telephone, with both giving a "high assessment of the resolution passed by the U.N. Security Council on the investigation into the catastrophe."
Meanwhile, European Union foreign ministers were scheduled on Tuesday to discuss further penalties against Russia, but the most they are expected to do is to speed up implementation of sanctions against individuals, and possibly companies, agreed in principle last week before the plane was brought down.
France is under pressure from Washington and London over plans to deliver a second helicopter carrier to Russia.
Diplomats say more serious sanctions against whole sectorsof the Russian economy will depend largely on the line taken bythe Dutch, because of the high number of Dutch victims.
"It is clear that Russia must use her influence on theseparatists to improve the situation on the ground," the Dutch prime minister said.
'What are they trying to hide?'
U.S. President Barack Obama said it was time for Putin and Russia "to pivot away from the strategy that they've been taking and get serious about trying to resolve hostilities within Ukraine."
He said Putin and Russia had a direct responsibility to compel separatists to cooperate with the investigation, and that the burden was on Moscow to insist that separatists stop tampering with the probe, he said.
"What are they trying to hide?" Obama said at the White House.
Australian Prime Minister Tony Abbott described what was happening at the scene as a cover-up.
"After the crime, comes the cover-up. What we have seen is evidence tampering on an industrial scale and obviously that has to stop," Abbott told reporters in Canberra on Tuesday.
Russia's Defence Ministry has challenged Western accusations that pro-Russian separatists were responsible for shooting down the airliner and said Ukrainian warplanes had flown close to it.
The ministry also rejected accusations that Russia had supplied the rebels with SA-11 Buk anti-aircraft missile systems - the weapon said by Kiev and the West to have downed the airliner - "or any other weapons".
Putin said the downing of the airliner must not be used for political ends and urged separatists to allow international experts access to the crash site.
His ambassador to Malaysia said the rebels did not trust the Ukrainian government and that was why they did not want to hand over the black boxes to them.
"This situation is quite unique, the area is a war zone. I think the international community should be flexible about that and act in a way acceptable to all sides," Lyudmila Vorobyeva said in a news conference.
The International Air Transport Association said governments should take the lead in reviewing how risk assessments for airspace are made after airlines called for a summit to discuss the downing of the airliner.
A guard stands on a train carrying the remains of victims of Malaysia Airlines MH17 downed over rebel-held territory in eastern Ukraine after it arrived in the city of Kharkiv, eastern Ukraine. (Reuters)
European security monitors said gunmen stopped theminspecting the site when they arrived on Friday, and Ukrainianofficials said separatists had tampered with vital evidence.
But the spokesman for the European security monitors saidthey had unfettered access on Monday, and three members of aDutch disaster victims identification team arrived at a railwaystation near the crash site and inspected the storage of thebodies in refrigerated rail cars.
Peter van Vliet, whose team went through the wagons dressedin surgical masks and rubber gloves, said he was impressed bythe work the recovery crews had done, given the heat and thescale of the crash site. "I think they did a hell of a job in ahell of a place," he said.
As they went about their work, fighting flared in Donetsk,some 60 km (40 miles) from the site, in a reminder ofthe dangers the experts face operating in a war zone.
Four people were killed in clashes, health officials said.
The rebels' military commander Igor Strelkov said on hisFacebook page up to 12 of his men died in Monday's fighting.