On 7 August 2014, following the coordination meeting held at Eurojust on 28 July, authorities from the Netherlands, Australia, Belgium and Ukraine signed an agreement to set up a joint investigation team (JIT) to investigate the crash of Malaysia Airlines Flight MH17, with the participation of Malaysia and Eurojust.
Malaysia was not invited to join the JIT. Which is very remarkable as the plane was operated by a Malaysian airline and also registered in Malaysia. Also 43 Malaysian people were among the dead.
The most likely reason for Malaysia not being a full member at the start was that Malaysia was too eager to investigate and bypassed Ukraine.
This is a reconstruction.
At August 7 an agreement was signed. This agreement has a non disclosure component. The existance of the agreement was secret for a long time.
At November 18 2014 Malaysia was still not invited to JIT. According Malayasia the Dutch had stated that also Ukraine and Australia had to approve the membership. (source)
Malaysia complained it was not allowed to recover the debris.
Finally at the end of November the Dutch sent a letter to Malaysia inviting the state to become a full member of JIT.
Dutch magazine Elsevier tried to request the JIT agreement. But the Dutch government refused to make the JIT-agreement public as the content could harm relations with other states (source)
At December 2 this was made public in Malaysian press.
At December 15 Malaysia was awaiting agreement from Eurojust after the country was accepted as a full member of the MH17 Joint Investigation Team (JIT). (source)
At the end of March 2015 a delegation of the Dutch prosecutor went to Malaysia to finalize the agreements with Malaysia on the full JIT membership. (source)
The reason why Malaysia was not permitted as full member to the JIT has never been made public. It could be because of Malaysia being neutral and did not want to point fingers to Russia as the culprit. Russia Today has some background here.
Another possible reason could be because Malaysia still has the death penalty. The Netherlands does not have. So this could be a conflict in joining JIT. (source)
A third possible reason could be the cooperation between Malaysia and the separatists. Malaysia was able to obtain the black boxes because of direct negotiations with the separatists. Ukraine did not want that and prevented the Netherlands to negotiate directly in order to recover the debris. The Netherlands always used OCSE to negotiate.
Malaysia announced at July 27 2014 that it has scored yet another agreement with the pro-Russia rebels controlling MH17’s crash site in Ukraine — this time to allow a group of international police personnel into the area to provide protection to air crash investigators.
Prime Minister Datuk Seri Najib Razak : “I hope that this agreement with Mr Borodai will ensure security on the ground, so the international investigators can conduct their work.”
At November 24 2015 the Malaysian deputy minister of Transportation admitted that Malaysia did not immediately give full cooperation in the DSB lead probe on the downing of Malaysia Airlines Flight MH17 until it was made a full member in the joint international investigation team. In the DSB final report is is clearly documented that DSB had a hard time to obtain information and speak to Malaysian people.
“Initially, Malaysia was not appointed fully in the joint investigation team,” Abdul Aziz explained to Parliament.
“Therefore, we gave a response that we would not cooperate until we were fully appointed in the JIT. Finally, Malaysia was made a full member of the JIT and we gave full cooperation in the investigation,” he added, using the initials for the joint investigation team. (source)