The train, with 16 representatives of the Netherlands, Malaysia and the Organisation for Security and Cooperation in Europe, had left the city of Donetsk, controlled by pro-Russian separatists, with 282 bodies and 87 remains of the 298 occupants of the ill-fated plane.
Flight MH17, while flying from Amsterdam to Kuala Lumpur, crashed last Thursday in the Donetsk region in eastern Ukraine, killing all 283 passengers and 15 crew on board.
Reports indicated that the Boeing 777 crashed after being hit by a missile. US President Barack Obama said initial investigations showed that the missile was fired from an area in Ukraine controlled by anti-Kiev militants.
On Tuesday, the convoy carrying the bodies arrived at the Kharkiv-Balashovski station and was expected to be transferred to a factory complex where the bodies will be put in special containers brought from Holland, Efe reported citing Interfax-Ukraine News Agency.
Dutch prime Minister Mark Rutte said the first victims of the crash will arrive Wednesday in the Netherlands, the country worst-hit by the crash, with 193 of the dead.
The train left the town of Torez, near the crash site, late Monday but stopped for several hours at the Donetsk station, where the pro-Russian separatists handed over the black boxes to a Malaysian representative.
"We did not come here to blame anyone. Both boxes are owned by Malaysia. At first glance you can see that the (black) boxes are intact", said the Malaysian colonel who headed his country's delegation.
Both the rebels and the Ukrainian government have blamed each other for the downing of the passenger jetliner.
Meanwhile, both Russia and Ukraine Tuesday welcomed a UN Security Council resolution, adopted at a meeting Monday, in which the Council members condemned "in the strongest terms" the downing of flight MHI7.
The resolution "demands that the armed groups in control of the crash site and the surrounding area refrain from any actions that may compromise the integrity of the crash site, including by refraining from destroying, moving, or disturbing wreckage, equipment, debris, personal belongings, or remains, and immediately provide safe, secure, full and unrestricted access to the site and surrounding area for the appropriate investigating authorities".
The Russia foreign ministry said that the resolution highlighted that the International Civil Aviation Organisation (ICAO) played a "crucial role" in a "completely independent and unbiased international investigation" and that Russia was ready to assist, the Russian foreign ministry said.
Moscow stressed that all confronting parties in Ukraine should stop fighting in the area and guarantee access to the crash site for the investigators, Organisation for Security and Cooperation in Europe (OSCE) monitors and other international organisations, Xinhua reported.
In Kiev, the Ukrainian foreign ministry, in a statement published on its website, said that Ukraine considered the result of the UN vote as unconditional support for a full, careful and independent international investigation.
Stressing that international experts should be given full access to the crash area and security guarantees during their work in Ukraine, the ministry called on the countries whose citizens were killed in the crash to consider the possibility of sending civilian police units to guard the site.
The foreign ministry emphasised that joint efforts by the international community to safeguard the crash area will allow a comprehensive and independent investigation into the incident.
Meanwhile, European Union countries Tuesday called for an arms embargo on Russia over the suspicion that Moscow provided heavy weaponry to the Ukrainian separatists, according to Efe.
Western countries believe Moscow could have supplied the sophisticated surface to air missile capable of hitting a plane at a cruise altitude of 33,000 feet.
Kiev had accused the separatists of tampering with evidence during the first days after the incident, when international investigators had only limited access to the crash site near the Russian border.
Fighting between the separatists and Ukrainian forces continued Tuesday, with 13 Ukrainian troopers killed in the troubled east of the country when a bus laden with explosives went off, the Ukrainian Defence and Security National Council reported.
Five civilians were also reported killed and 16 were wounded in heavy shelling on the eastern city of Luhansk, controlled by the rebels.