The airline said contact has been established with the man in command of the region, Alexander Borodai.
In a statement, Malaysian Prime Minister Najib Razak said: "Under difficult and fluid circumstances, we have been discussing the problems that have occupied us all: securing vital evidence from the aircraft, launching an independent investigation, and above all recovering the remains of those who lost their lives."
The PM said the following has been agreed:
Firstly, the remains of 282 people, currently in Torez, will be moved by train to Kharkiv, where they will be handed over to representatives from the Netherlands. The remains will then be flown to Amsterdam on board a Dutch C130 Hercules, together with members of the Malaysian team.
Following any necessary forensic work, the remains of Malaysian citizens will then be flown home to Malaysia.
Secondly, the two black boxes will be handed over to a Malaysian team in Donetsk, who will take custody of them.
Thirdly, independent international investigators will be guaranteed safe access to the crash site to begin a full investigation of the incident.
The Malaysian leader urged all parties to continue to work together "to ensure that this agreement is honoured; that the remains of our people are returned, that the black box is handed over, and that the international team is granted full access to the site".
"Only then," he added, "can the investigation into MH17 truly begin; only then can the victims be afforded the respect they deserve.
"We need to know what caused the plane to crash, and who was responsible for it, so that justice may be done."
The prime minister added: "In recent days, there were times I wanted to give greater voice to the anger and grief that the Malaysian people feel. And that I feel.
"But sometimes, we must work quietly in the service of a better outcome."
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