NYT noted that Prime Minister Datuk Seri Najib Tun Razak said in a live television broadcast early Tuesday that the agreement with Alexander Borodai, a commander of the separatist forces in Donetsk, Ukraine, called for the bodies of the victims to be taken by train to Kharkiv, a city held by the Ukrainian government.
Six Malaysian representatives were to oversee the transfer of the bodies in Kharkiv to Dutch custody.
Under the agreement, the bodies and the Malaysian representatives would then be flown in a Dutch C-130 Hercules transport plane to the Netherlands for identification and repatriation of remains.
NYT said if all participants honour the deal, it would be a diplomatic success for Malaysia.
"Mr Najib said that at times over the past few days he had wanted to be more outspoken about events in Ukraine, “but sometimes, we must work quietly in the service of a better outcome.”
"The agreement is the result of an unusual spate of diplomacy by Mr Najib, who held a series of secret telephone calls with Mr Borodai.
"A person with a detailed knowledge of the negotiations said that Mr Borodai concluded that he would only release the bodies and black boxes to Malaysia, although Malaysia would then transfer the bodies to the Netherlands and make the black boxes available for an international investigation.
"The backdrop for the negotiations was a slowly growing criticism within Malaysia, including by some in the political opposition, that Mr Najib did not appear to be more publicly critical of the separatists or Russia," NYT said.
It said the agreement with the separatists followed four days of sometimes frenetic diplomacy in which a series of senior Malaysian officials, including the country’s foreign minister and transport minister, rushed to Kiev, Moscow and Amsterdam to broker a deal.
NYT said Malaysia, and particularly Mr Najib, have played an outsize role in diplomatic agreements in Southeast Asia in recent years, and tried to apply those skills to dealing with the separatists.
It said Malaysia has an enormous stake in resolving the problems that have impeded a prompt investigation of the crash and the quick recovery of the 298 victims, who are exposed to abuse and tampering.
"As well, Malaysia was already struggling with the unexplained loss of Malaysia Airlines Flight 370, still missing more than four months after it disappeared after turning from its planned course," it added.
However, NYT questioned why the separatists chose to deal with Malaysia when they were under pressure by many big nations like United States, Australia and Britain to release the bodies and surrender the black boxes.
“A big question, which was not immediately clear, was why the Ukrainian separatists chose to deal with the Malaysians at a time when the separatists were under pressure by many countries to release the bodies and surrender the black boxes,” it said.
Sydney Morning Herald also touched on Najib’s technique in reaching the agreement and said the tragedy was deeply personal as his step-grandmother was on board the plane.
“After cautiously refusing to blame pro-Russian rebels for shooting down MH17, Malaysia’s Prime Minister Najib Razak used secret diplomacy to reach an agreement for the transfer of the bodies and black box recording devices from the plane to Malaysian representatives.
“Mr Najib has been criticised in Malaysia for failing to directly blame the separatists for bringing down the plane as anger grew across the country about the lack of dignity for the bodies, 43 of whom were Malaysians.
“But he instead held a series of secret telephone calls with Mr Borodai who is believed to have said he would only hand over the bodies and black boxes to Malaysia,” said Southeast Asia correspondent Lindsay Murdoch for Fairfax Media.