Three Royal Navy ships containing human remains are believed to have been illegally salvaged for scrap metal, as well as three Dutch vessels and a US submarine.
All were sunk when the Japanese defeated a joint British, American, Australian and Dutch fleet in the Battle of the Java Sea.
As many as 2,300 Allied servicemen were killed.
An expedition to document sunken ships reportedly showed that HMS Exeter and HMS Encounter had been almost totally removed form the sea bed.
Another destroyer, HMS Electra, had also been looted, although much of it remains.
The Dutch defence ministry has begun its own investigation into the disappearance of three of its vessels.
The US submarine USS Perch has also been removed.
"The UK government condemns the unauthorised disturbance of any wreck containing human remains," said the MoD.
"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."
The MoD said international law protects war graves and it would expect them to be left undisturbed.
"Desecration of wrecks of war and merchant vessels causes distress to loved ones of those lost on board ... The desecration of a war grave is a serious offence," it said.
The MoD said it would continue to work with governments to prevent "inappropriate activity".
"A military wreck should remain undisturbed and those who lost their lives on board should be allowed to rest in peace," said the MoD.
"Where we have evidence of desecration of these sites, we will take appropriate action."
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