The Dutch queen was accompanied by her husband King Willem-Alexander and the Dutch Prime Minister Mark Rutte.
Throughout the ceremony the royal couple held each other's hands tight as the coffins were brought off the plane.
Last week's devastating incident saw 298 people killed when flight MH17 crashed in eastern Ukraine after taking off from Amsterdam.
The majority of the passengers were Dutch and Wednesday was declared a national day of mourning for the Netherlands.
The king and queen have met family members of the deceased this past week, and last Friday the couple signed the book of condolences that has been placed outside of the Ministry of Security and Justice in the Hague, Netherlands.
A second book has also been set up outside of Schiphol Airport where the flight took off from on 17 July.
Princess Mabel van Oranje, the king and queen of the Netherlands sister-in-law, has also spoken out about the shocking events.
"My thoughts go out to all those families, friends and colleagues have lost. So pointless. Such a tragedy. # MH17" she tweeted
Britain's Prince William last week gave a statement on the tragedy. "For all of us who have lost countrymen and women in the tragedy, words cannot do justice to our sense of loss," William said.