The Inquiry was set up after criticism of the Secretary of State for Defence, and the MoD by three high Court judges. After the allegations were made, instead of fully investigating them and refute them, they attempted to gag and be uncooperative in attempting to find the truth. That angered the Judges who were highly critical and the Inquiry was ordered soon afterwards.
From a Guardian report in 2009
// "We are forced to the conclusion that the approach of the secretary of state to disclosure in this case was lamentable," Lord Justice Scott Baker, Mr Justice Silber and Mr Justice Sweeney ruled today.
They said that when he was armed forces minister earlier this year Ainsworth signed a demand for a gagging order even though the information he sought to suppress had already been published. The matter caused the judges "very considerable concern", they said.
Over more than eight months, "the secretary of state's agents had simply failed for no good reason during that lengthy period to carry out these critically important and obviously highly relevant searches [for documents]", the judges added.
They singled out Colonel Dudley Giles, deputy provost marshal – deputy head of the military police – for "lamentable disclosure failures". Asked why he had not referred in his witness statement to a document stating that the soldiers had detained between 10 and 12 Iraqi detainees, Giles replied that he did so to avoid prejudicing any future prosecution.
"When this assertion was examined, it became obvious that it was wholly without foundation," said the judges. //
http://www.theguardian.com/politics/2009/oct/02/ministry-of-defence-shamed-iraq
If the MoD had cooperated at the onset of these allegations, this costly Inquiry would never have been needed.