The team planned to place a plaque next to the wreck of a Dutch admiral's warship to commemorate the upcoming 75th anniversary of its sinking.
Instead, the expedition made a startling discovery.
"We were and are all shocked that the ships were gone," said Lt. Cmdr. Paul Middelberg, a spokesman for the Dutch Ministry of Defense.
The wrecks of the admiral's ship, the cruiser HNMLS De Ruyter and another Dutch cruiser, HNLMS Java, had completely disappeared. Most of the remains of the Dutch destroyer HNLMS Kortenaer were also missing.
According to the Dutch Ministry of Defense, "divers did find tracks and sonar recordings showing the imprints of ships at the bottom of the sea."
And it wasn't only Dutch warships that disappeared.
All traces of at least two British warships that also sank in the Battle of Java Sea apparently had apparently also gone missing, Middelberg said.
The British and Dutch governments issued public condemnations.
The US Navy also released a statement expressing concern "that the wreck of the USS Perch, a sovereign vessel, has been salvaged without the permission or knowledge of the US government."
The USS Perch -- a submarine -- was one of at least eight vessels to be sunk in one of the worst naval defeats the Allies faced during World War II.
The battle began on February 27, 1942, when the Dutch Adm. Karel Doorman led a coalition fleet of American, Dutch, British and Australian warships in an effort to protect Dutch-ruled Indonesia from invasion by Japan.
Throughout several days of clashes, the Japanese decimated the Allied fleet.
Doorman died aboard his flagship after the cruiser was sunk by a Japanese torpedo.
The Japanese fleet also sank the Dutch ships Java and Kortenaer, the British destroyers HMS Jupiter, HMS Electra and cruiser HMS Exeter, as well as the US submarine Perch.
In a battle in the nearby Sunda Strait on March 1, 1942, Japanese ships succeeded in sinking the vastly outnumbered Australian cruiser HMAS Perth and USS Houston, which had been the flagship of the US Asiatic Fleet.
Thousands of sailors died with their ships.
"There were so many fatalities during that early part of World War II, it is just mind-boggling how many sunken ships there are in that area, " said John Schwarz, executive director of the USS Houston Survivors' Association and Next Generations.
In 1942, Schwarz's father Otto was a teenage sailor aboard the Houston who barely survived its sinking.
"He literally was the only person who got out of the lower deck turret number one team, because he was a young man only 17-years-old," Schwarz said.
"Any untold hundreds of (sailors) literally went down with the ship including many who may have been sealed off in sealed compartments," he added.
The shipwrecks had all been located within the waters of Indonesia's exclusive economic zone.
Senior Indonesian officials appeared baffled by their disappearance.
"It hasn't been identified whether it has moved or it has been stolen," Indonesian Foreign Ministry spokesman Arrmanatha Nasir told CNN.
"The point is it is not there, where it once was there," he added, suggesting the wrecks may have somehow "shifted" on their own underwater.
The Indonesian government has agreed to work with Dutch authorities on a joint investigation into the matter.
"The problem in southeast Asia is that there's a lot of looting," said Mark Staniforth, a marine archaeologist with Flinders University in Australia.
"Somebody has been salvaging metal from naval vessels in the region of Indonesia for years," he added.
In 2014, the US Navy discovered "systematic and ongoing disturbance" of the wreck of the Houston during a diving expedition.
Looters had ripped out the majority of the Houston's portholes, removed rivets holding the ship's hull together, and had been in the process of gathering unexploded shells and ordnance.
Valuable scrap metal
Academics and workers in the Indonesian ship salvage industry tell CNN that the precious and scrap metals that can be scavenged from a shipwreck can be worth hundreds of thousands of dollars.
"The bronze propellers off of larger vessels are worth 40 to 50 thousands dollars," said Professor Staniforth.
According to the Dutch-led diving expedition, in addition to the missing ships, the propellers from the wreck of the British destroyer Electra had been removed.
Shipbreakers on the Indonesian island of Madura who make a living harvesting metal from retired ships explained in detail how a wreck could be lifted from the bottom of the Java Sea.
"You need compressors to breath underwater using tubes. To cut the metal, you need an underwater electric weld. After cutting the pieces, you use a crane to haul them up to the surface," said Mulyadi, a crew manager at a junk shipyard in Madura.
But he said the cost of pulling an entire shipwreck from estimated depths of 60 meters below sea level would be prohibitive.
"The problem is the waters are too deep," he said.
While the US Navy says it is working with the Indonesian government to protect the Houston from further looting, news of the possible scavenging of entire World War II shipwrecks have devastated some veterans' organizations.
"We are on egg-shells," said John Schwarz of the Houston Survivors' Association.
"We're just praying and hoping that no further damage gets done to either our ship or any others."
Undersea war grave
"Wrecks of warships are the final resting place of killed soldiers and are therefore war graves," said the Dutch Ministry of Defense in a statement last month.
"Desecration is a serious offense," it added.
Veterans' groups say the shipwrecks should be protected much like any other cemetery holding the graves of fallen servicemen and women.
John Schwarz, whose father founded the USS Houston Survivors' Association, argued that scavenging wrecks that are believed to hold the remains of hundreds of sailors would be the same as "going into Arlington National Cemetery with excavating equipment, and digging up coffins and graves."
"It is truly a sacred burial ground," Schwarz said.
He urged the Indonesian government to do its part "to protect the sanctity of those ships."