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Divers first found the WWII wrecks -- which were declared war graves -- off the coast of Indonesia in 2002.
Though divers used underwater photography and sonar to find traces of where the ships had been, both cruisers and vast parts of the destroyer had disappeared from the bottom of the Java Sea.
The Guardian also reported that two British ships, the heavy 8,390-ton cruiser HMS Exeter and the 1,405-ton destroyer HMS Encounter, and one US Navy submarine had also gone missing. HMS Electra, a 1,405-ton British destroyer, has also been scavenged though a chunk of that wreck still remains.
"The [Dutch] MOD very much deplores the fact the ships are gone. After all, we have to treat this matter with care, we are talking about a very important war grave," a Dutch MOD spokesman told CNN.
The Battle of the Java Sea -- which marked the height of Japanese naval power in the Pacific -- involved British, Dutch, US and Australian ships and took place on February 27, 1942. It proved disastrous for allied forces who suffered the loss of at least 10 ships and 2,173 sailors.
Ships stripped for metal?
"The UK government condemns the unauthorized disturbance of any wreck containing human remains," a spokesperson from the British Ministry of Defense, told CNN in a statement.
"We have contacted the Indonesian authorities to express our serious concern at this news and to request that they investigate the reports and take appropriate action to protect the sites from any further disturbance."
It is against international law to desecrate naval war wrecks, war graves and associated artifacts as it causes distress to loved ones of those who lost their lives on board.
The British Ministry of Defense added that it would continue to work with regional governments and partners to prevent inappropriate and unauthorized activity on the wrecks of Royal Navy vessels.
"A military wreck should remain undisturbed and those who lost their lives on board should be allowed to rest in peace," the British MOD added.