File Photo- A Lockheed Martin F-35 fighting jet is pictured at the ILA Berlin Air Show.AFP
The groups had argued that supplying the parts contributed to violations of international law by Israel in its war on Gaza.
"The court orders the State to cease all actual export and transit of F-35 parts with final destination Israel within seven days after service of this judgment," said the ruling.
The US-owned F-35 parts are stored at a warehouse in the Netherlands and then shipped to several partners, including Israel, via existing export agreements.
"In doing so, the Netherlands is contributing to serious violations of humanitarian law of war in Gaza," the rights groups argue.
In December, the district court in The Hague had said that supplying the parts was primarily a political decision that judges should not interfere with.
"The considerations that the minister makes are to a large extent of a political and policy nature and judges should leave the minister a large amount of freedom," the court ruled at the time.
Dutch authorities had said it was not clear whether they even had the power to intervene in the deliveries, part of a US-run operation that supplies parts to all F-35 partners.
The International Court of Justice in The Hague, which rules on disputes between states, has said Israel must do everything possible to prevent genocidal acts in Gaza.
That ruling "strengthens our confidence in a positive ruling in our case", said PAX Netherlands, one of the rights groups involved in the appeal.