Marine Colonel Matthew Bogdanos said on Wednesday that among the stolen items was a priceless Sumerian mask.
He said more than 10,000 of the stolen items are still missing, noting that a full inventory of the museum's vast collection is yet to be completed five months after the end of the war.
"But it is clear that the originally reported number of 170,000 (stolen artifacts) was simply wrong," he added.
Museum staff removed the bulk of the treasures from public galleries before the war and hid them in the central bank's vaults, a bomb shelter, and another secret location for safekeeping.
They have since been accounted for, Bogdanos said.
The missing items include 30 pieces from its public galleries, including a statue from 2300 BC and Roman heads of Poseidon, Apollo, Nike and Eros.
Bogdanos, who has submitted his investigation report to the chief of the US Central Command, said "numbers cannot tell the whole story".
"For example, it is impossible to quantify the loss of one of the world's first known marble masks, in this case the mask of a Sumerian female diety or priestess from Warka."
Museum insiders made off with most of the loot, breaking into a basement storage room and going straight for a row of cabinets containing one of the world's finest collections of cylinder seals and ancient coins.
The collection was spared because the thieves dropped keys to the cabinets in the darkened room.
But they emptied 103 other small plastic boxes containing less valuable cylinder seals, loose beads, amulets, small glass bottles and jewellery.
"There is no evidence whatsoever that any US forces had anything to do with any of the looting and none of the fingerprints that we found match any US forces"
Colonel Matthew Bogdanos
"From this single room alone, 10,337 separate items were stolen, of which 667 have been recovered," said Bogdanos.
He said it was "simply inconceivable" that the theft was not carried out by someone with inside knowledge of the museum, its storage practices and in possession of unmarked keys to the cabinets.
Bogdanos said several sets of readable fingerprints were recovered from cabinet doors.
The fingerprints were compared to those in all known US databases, including US military files, as well as to fingerprints taken from museum staff, but no matches were found.
"There is no evidence whatsoever that any US forces had anything to do with any of the looting and none of the fingerprints that we found match any US forces," he said.
While no matches were found with museum staff, some former members of the staff disappeared after the war, he said.
Bogdanos said items stolen from storage rooms on the museum's first and second floors were taken by looters who made off with 2703 pieces from excavation sites.
All but 254 were later returned under an amnesty and appeals for their return.
Investigations are underway in four countries as part of an international effort to track down missing pieces on the black market in antiquities.
"The majority of the work remaining - that of tracking down each of the missing pieces - will likely take years," Bogdanos said.