"It is possibly one of the largest thefts in history," the paper said in its Monday edition, quoting Iraqi Finance Minister Ali Allawi as saying.
Most of the money was "siphoned abroad in cash and has disappeared" to finance the purchase of arms in Poland and Pakistan, according to the report.
But rather than purchasing state-of-the-art weaponry Iraq had procured "museum-piece weapons," the Independent charged.
The paper listed a series of problems with the arms purchased including armoured cars which "turned out to be so poorly made that even a bullet from an elderly AK-47 machine-gun could penetrate their armour."
Other armoured cars reportedly leaked so much oil that they had to be abandoned.
A shipment of the latest MP5 American machine-guns turned out to be Egyptian copies worth a fraction of the price, according to the report.
"Many Iraqi soldiers and police have died because they were not properly equipped," the daily added.
The rip-offs were so huge, said the paper, that Baghdad officials estimate that the Iraqis involved "were only front men.
Furthermore, 'rogue elements' within the US military and intelligence services may have played a decisive role behind the scenes".
Iraqi Prime Minister Ibrahim al-Jaafari has been informed of the problem "but the extent of the losses has become apparent only gradually. The sum missing was first reported as $300 million and then $500 million, but in fact it is at least twice as large," the paper said.
"It is nearly 100% of the ministry's (procurement) budget that has gone AWOL (absent without leave)," Allawi was quoted as saying.
Allawi says a further $500-600 million has allegedly disappeared from the electricity, transport, interior and other ministries.
"This helps to explain why the supply of electricity in Baghdad has been so poor since the fall of Saddam Hussein 29 months ago despite claims by the US and subsequent Iraqi governments that they are doing everything to improve power generation."