Indonesian and Dutch experts have “examined all the available data” and concluded the wrecks must have been taken from the bottom of the Java Sea, the Dutch foreign ministry said.
The disappearance of the wrecks was first noticed in 2016 when an international expedition was sent to the spot to prepare for commemorations to mark the 75th anniversary of the sea battle in which they foundered.
It is believed they were illegally salvaged by people seeking to remove valuable metal.
Experts have recommended that a full inquiry now be opened “to gather extra information” including about those responsible.
The ministry stressed that an accord has been reached with Jakarta to share information and knowledge “to protect cultural maritime heritage.”
There are about a dozen Dutch wrecks in the region some of which date back to the 17th century, ministry spokesman Paul Middelberg told AFP.
The warships De Ruyter, Java and Kortenaer sank during a major World War II battle on February 27, 1942, leading to the deaths of some 915 troops.
Two British warships, which also sank in the same firefight, have also disappeared, according to British daily The Guardian.
Dozens of wrecks are still believed to languish at the bottom of the Java Sea, between the islands of Java and Borneo. It was the scene of one of the most decisive battles of the Pacific Campaign during World War II when the invading Japanese navy defeated the Allied forces.