"Interfering with the scene of the crash risks undermining the investigation itself. Any actions that prevent us from learning the truth about what happened to MH17 cannot be tolerated," Malaysian Transport minister Liow Tiong Lai said in a statement.
"Failure to stop such interference would be a betrayal of the lives that were lost," he added.
The Boeing 777 was flying from Amsterdam to Kuala Lumpur as it was downed between Krasni Luch in Luhansk region and Shakhtarsk in the neighbouring region of Donetsk.
Malaysian Transport minister Liow called for all parties to protect the integrity of the crash site and to allow the investigation to proceed.
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"We urge all those involved to respect the families and the nations who have lost their sons and daughters in this attack," he added.
Malaysia sent a special team to Kiev to assist the Ukrainian authorities for recovering and identifying the remains of the passengers and crew, Malaysia's national news agency Bernama reported.
"MH17's flight path was a busy major airway, like a highway in the sky. It followed a route which was set out by the international aviation authorities, approved by Eurocontrol, and used by hundreds of other aircraft," he said.
Liow said that officials from Eurocontrol stated that in the two days before the incident, 75 different airlines had flown by the same route.
"MH17 flew at an altitude that was set and deemed safe by local air traffic control, and it never strayed into restricted airspace", the minister said.