The wreckage, collected by local emergency services under Dutch supervision in an area fought over by Russian-backed rebels and troops loyal to the Kiev government, will be trucked to the air base next week.
The aircraft debris lay there for months after the Boeing 777 was downed on July 17, killing all 298 people on board, because outside investigators had difficulty entering the area.
Investigators and prosecutors believe the plane was likely shot down by a ground-to-air missile but are open to Moscow's theory that it was shot down from the air.
"The Defence Ministry has prepared the transportation of the wreckage and the loading of the first lorries will start today," the Dutch Safety Board said in a statement.
Some human remains that were only recently recovered were flown back to the Netherlands on Friday, where they have been taken to another military base to be identified.
More than two-thirds of those on board the flight from Amsterdam to Kuala Lumpur were Dutch, and Dutch authorities have taken the lead in the investigations into the airliner's downing.
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