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Members of the national Safety Board will piece together the remains of the plane on a frame to determine exactly what brought down flight MH17 and killed all 298 people on board.
It will take several months to complete the reconstruction and a final report on the cause of the crash is not expected until mid-2015, Safety Board head Tjibbe Joustra said.
The task will not be easy, with some parts of the aircraft having been destroyed by fire.
"There were also some parts missing. We know that they were missing, but we think that we can be more than satisfied about the amount of wreckage we have."
A parallel criminal investigation is being conducted by Dutch prosecutors in 11 countries to identify possible culprits. Two-thirds of the passengers on board the flight from Amsterdam to Kuala Lumpur were Dutch.
Washington and its allies said pro-Russian rebels fighting in the area hit the plane with a surface-to-air missile. Russia, caught up in its worst confrontation with the West since the Cold War, said the missile came from a Ukrainian government jet.
Dozens of relatives of the victims looked on in the southern town of Gilze-Rijen as eight flatbed trucks pulled into the military base under police escort.
Ukrainian emergency services operating under Dutch supervision picked up wreckage considered most valuable for the inquiry during a six-day operation in November. Bits of fuselage could help determine what direction the missile came from.
Grieving families have protested against delays in the investigation after debris lay strewn across the crash site for months.
On Tuesday, the Dutch government rejected a call by one group of relatives for a U.N. envoy to take over the investigation, saying the investigation already involved officials from 11 different countries.
The relatives had accused Dutch authorities of leading a "botched" investigation.
The wreckage was transferred under a deal with Kiev and, through mediation by the Organisation for Security and Cooperation in Europe (OSCE), pro-Russian separatists.
The Dutch Safety Board said the wreckage would be photographed, scanned and categorized and experts would then attempt to reconstruct the airliner.