The former shareholders immediately vowed to continue their legal battle for compensation and to appeal the decision.
The Hague District Court's written ruling overturned a July 2014 decision by the Permanent Court of Arbitration, which said that Moscow used massive tax claims to seize control of Yukos in 2003 and silence its CEO, Mikhail Khodorkovsky.
Khodorkovsky, an opponent of President Vladimir Putin, had begun to use his vast wealth to fund opposition parties challenging Putin's power.
Tim Osborne, director of GML, the company that indirectly owned the majority of Yukos' shares, said the company maintained that the 2014 award for what he called the "politically motivated destruction of Yukos" was right.
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"We will appeal this surprise decision by The Hague Court and have full faith that the rule of law and justice will ultimately prevail," he said in a statement.
Lawyers for the former shareholders said that regardless of the Dutch court's ruling they would continue efforts they have started in several countries to enforce the arbitration award by attempting to seize Russian assets in countries including the United States, the United Kingdom, France, Belgium, Germany and India.
That tactic also has run into legal hurdles. Last week, a French court invalidated the seizure last July of 400 million euros that French company Eutelsat owed to Russian company RSCC for satellite cooperation deals. The French judge also annulled seizures at news agency RIA Novosti, now called Sputnik, and the Russian agency for management of state property abroad.