Fifty museum employees staged a protest in which they waved placards under the noses of American investigators proclaiming that Jabir Khalil, chairman of the Iraqi state board of heritage and antiquities, was a “dictator” and a “thief”.

Another museum director tried to calm the protesters, calling their allegations against their boss “stupid” and baseless. “In any case, there are proper procedures for investigating these matters,” said Donny George, the museum’s head of research.

The protesters dribbled back to their offices under the gaze of the American investigators, including customs agents and soldiers, who have installed themselves in an adjacent building while conducting inquiries.

The investigators, too, have expressed suspicions that the plunder was facilitated by museum employees. Objects had vanished from a storage vault outside the museum to which museum officials had access. “It may turn out to be an inside job,” said one investigator. “Whoever did this seemed to know exactly what they were looking for.”

A full account of what is missing has yet to be given. Even so, officials concede that the losses may be less severe than at first thought, when talk of looters carting off thousands of ancient carvings and crushing pottery underfoot prompted international outrage at America’s failure to intervene.

Since then, indignation has been fuelled by suggestions that some of the thieves were directed by professional collectors abroad. Museums around the world have pledged not to trade in items that may have been stolen in Baghdad.

Suspicions about the involvement of staff with knowledge of the underground vaults are growing. “Looters went into the storerooms, to a specific area, and removed small items of high value,” said George. “It shows a certain knowledge.”

However, he stopped short of accusing colleagues of consenting to the plunder, saying the investigation had yet to determine how the thieves broke in.

He said initial reports on the scale of the losses had been deeply misleading. “The whole museum collection includes about 170,000 items but somehow this ended up being reported as the number of pieces that had been stolen. It is nothing like that.”

In fact, he said, a large quantity of pieces had been removed for safekeeping before the war. Only between 30 and 35 items — including a famous Uruk vase decorated with pictures of sheep, goats and priests and dating from about 3500BC — had been stolen from the museum’s exhibition area.

American investigators think the number of items missing from storage is several hundred. The task of tracking the artefacts is complicated by the fact that thousands of objects in storage had never been catalogued or photographed, making them a tempting target for professionals hoping to profit from sales on the international black market.

“Even if they have a little museum mark on the back of them, that can easily be removed,” said Neil MacGregor, director of the British Museum.

Iraqi museum staff have been heartened by the recovery of hundreds of missing items in recent days, some of them anonymously delivered to mosques after appeals from religious leaders. Others have been brought to the museum by individuals who claim they witnessed the looting and decided to take items home to protect them from thieves.

These have included the stone statue of King Shalmaneser III from the 9th century BC — “a remarkable piece”, said George. Also returned was a series of bronze reliefs from the Sumerian period of about 3500BC and some “excellent” pieces of Assyrian pottery that might have fetched high prices overseas.

“Almost every day we get something back,” said George. The Americans have offered an amnesty to Iraqis who returned objects looted from the museum, and have recovered about 450 pieces in recent days.

These include a vase reported to date from the 5th century BC and a broken statue of an Assyrian king from about 900BC.

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