The glittering treasures stashed at the site are at the centre of a shadowy scandal entwining accused modern-day pirates, booty worth millions of dollars, stern diplomatic protests and murky corruption allegations.
At risk, experts say, is priceless Indonesian history.
Timber and iron beams from a 10th-century wreck - which could provide information about ancient trading routes and the arrival of Islam in Indonesia - lie in a bath under the tropical sun behind yellow police tape.
Several thousand centuries-old Chinese ceramic bowls are stacked in plastic crates.
Under a nearby hangar, fragile copper mirrors, beautiful glass bottles and ancient ship parts are also being stored as the drama outside unfolds.
Last month police swooped in the middle of the night on two divers, German Fred Dobberphul and Frenchman Jean-Paul Blancan, accusing them of illegally salvaging their find during some 24,000 dives made over more than a year-long period.
Anton Bachrul Alam, the deputy national police spokesman, said: "Blancan doesn't have a licence to do that, only PT Paradigma does."
He was referring to the Indonesian salvage company that employed them.
Divers Fred Dobberphul and Jean-
Paul Blancan have been detained
Their lawyer Yudhistira Setiawan denies the claim, pointing out that both divers have work visas as employees of the company and kept authorities fully informed of their excavation work.
Blancan is now in an Indonesian prison hospital, suffering from typhoid and dengue fever, after being shifted from his cell with Dobberphul. The pair face up to 10 years' imprisonment.
A furious Blancan said during a telephone interview last week that "it is incomprehensible and scandalous. It concerns disrespect of freedom and of human rights".
Cultural heritage laws
Both the German and French embassies in Indonesia have said that the salvage operations had the necessary permits from at least 11 ministries. The French embassy issued a protest note saying that Blancan's arrest was arbitrary.
Police say their charges are based on a 1992 law on cultural heritage, but the company's lawyer and marine ministry say this was superceded by a 2000 presidential decree aimed at making treasure-hunting transparent.
Under the decree, a salvage company receives a license to retrieve a wreck's contents and returns 50% of its earnings to the Indonesia government.
The ship's cargo sheds light on the
earliest arrival of Islam in region
Luc Heymans, the Belgian head of the salvaging project begun two years ago, claims that a rival company, PT Tuban Oceanic Research and Recovery (TORR), was behind the arrests, aiming to get their own hands on the bounty.
He alleges that corrupt elements in the Indonesian police - who work in a country regularly rated as one of the most graft-prone in the world - have assisted his rivals.
When asked about the corruption allegations, police insisted their investigation followed the 1992 law while Budi Prakosa, director of TORR, has denied that his company wants to take over their work.
Prakosa told local investigative weekly Gatra last month that he had reported Heymans and his team to the marine ministry because he had "concrete data" about their illegality.
Indonesia's Agency for the Protection of Underwater Heritage, a government body that coordinates the complex issuing of permits for salvage operations, has sent repeated letters to police arguing that Heymans' team was legal, agency head Hasyim Zaini told
"We already checked the process for Paradigma, and we know it followed the rules and procedures for excavation," he said.
Each week the imbroglio drags on, Indonesia is at risk of losing a key portion of its maritime history, experts warn.
After sitting under the ocean for a thousand years, the treasures urgently need complex preservation treatments, Heymans said.
"Some of the artefacts are in great danger if the government doesn't open up the warehouse. The bronze pieces are in danger of eroding," he said.
"They are losing answers to (questions about) the Java and Srivijaya kingdoms, some of the richest kingdoms of their time"
Of particular concern are some fragments of the ship's structural timbers and iron bars, which are sitting in salty water in a desalination tank - originally a horse bath - open to the elements beside the warehouse.
Horst Liebner, a maritime historian advising the marine ministry, said that while the fragments are not financially valuable, they provide important clues to trade between Indonesian kingdoms, Persia, Africa, and China.
"They are losing answers to (questions about) the Java and Srivijaya kingdoms, some of the richest kingdoms of their time," said Liebner, referring to early Indonesian maritime kingdoms flourishing between the 7th and 12th centuries.
Horst said preliminary research into the ship's cargo contested prior theories about the earliest arrival of Islam in the archipelago.
Tenth century wrecks, particularly with cargo from Egypt, China and Persia, are extremely rare, said Catherine Noppe, a curator of Belgium's Far Eastern Art at the Royal Museum of Mariemont.
"There are a lot of more recent shipwrecks, but nothing that could be compared with the Cirebon shipwreck," Noppe, who provided scientific advice to the salvage team, told AFP in an email.
Cirebon, near the location of the wreck, is located about 200km east of Jakarta and was once an important regional Islamic port.
Heymans' wreck is among more than a thousand believed sunk off the coasts of Java and Sumatra.
Heymans and the marine ministry have asked both police and the Indonesian president for permission to continue the desalination and preservation process while the police investigation continues.
Asked whether police were concerned that Indonesia's early history was disintegrating behind police lines, spokesman Bachrul replied curtly: "That's their opinion."