Holes are shot in army's denial of Gaza attack

Doubts have been cast on the Israeli rebuttal of the Goldstone Report, after it emerged last night that a bomb was defused last year at a Gaza flour mill that Israel had officially said did not come under air attack in the war.

The presence of a large part of the fractured Mark 82 bomb was reported to a demining team in late January 2009, and technicians were dispatched to defuse the 500lb device on 11 February.

The flour mill is the only one in Gaza, and the Goldstone Report, commissioned by the United Nations, said its destruction "was carried out for the purpose of denying sustenance to the civilian population".

The discrepancy came to light on a day in which domestic and international debate over the Goldstone Report and Israel's response was fuelled by a reprimand issued to two high-ranking officers.

Israel said a brigadier-general and a colonel had "exceeded their authority in a manner that jeopardised the lives of others" by authorising the firing of artillery shells into the area of the main UN compound in Gaza. The Israeli military denied a Haaretz report that the two had been reprimanded over the use of white phosphorus.

UN officials had described how the attack – which destroyed the UN warehouse – scattered burning white phosphorus through the compound.

The government of Prime Minister Benjamin Netanyahu is trying to decide whether to order an independent investigation into the Gaza offensive or face the possible fresh moves, threatened in the Goldstone Report, for an external war crimes inquiry to be launched.

The case of the El Badr flour mill in northern Gaza was examined in detail in the 575-page report by the Jewish South African judge, Richard Goldstone. It said the mill had come under air as well as ground attack during Operation Cast Lead, which lasted for three weeks last winter.

The official update of Israel's own investigations – sent to the UN on Friday – says that inquiries by the military's Advocate General had found that the mill did come under ground attack, but that he "did not find any evidence to support the assertion that the mill was attacked from the air using precise munitions".

It said that the military's Advocate General had "determined that the allegation was not supported in the [Goldstone] report itself, nor in the testimony to the Fact-Finding Mission by [the joint owner] Rashad Hamada, who had left the area prior to the incident in response to the IDF's early warnings."

But an international mines action team went to the flour mill on 11 February 2009 to take the fuse out of the unexploded front half of the bomb – the sort commonly carried by Israeli Air Force F16 aircraft – both a UN technical source and Mahmoud Hamada, brother of Rashad, confirmed to The Independent last night.

The Israeli report to the UN says that from the beginning of the Gaza operation the immediate area of the flour mill was used as a defensive zone because of its "proximity to Hamas's stronghold in the Shati refugee camp". It said that Hamas had fortified the area with tunnels, booby-trapped houses, and had deployed its forces to attack troops operating there. One IDF squad had been ambushed by five Hamas operatives in a booby-trapped house.

But while saying that the mill had come under fire during the engagements, Israel rejected the suggestion in the Goldstone Report that it had come under deliberate attack, and said that photographic evidence of the building was not consistent with an air attack.

Mahmoud Hamada said last night that the 110cm-long front of the bomb had mercifully not exploded but had destroyed a 4-tonne milling machine. He did not know what had happened to the other half but thought it might have exploded in the air.

Deadly and cheap: The Mark 82 bomb

Developed in the 1950s, the Mark 82 is aerodynamic, deadly and cheap. One of the most common bombs dropped in the world – Israel's air force drops them from F-16 jets – and costing less than $300 (£190) to produce, each general-purpose 500lb bomb has a blast radius of about 40ft. In the Gaza conflict, Israel is said to have used a fin-guided version with parts made by US arms manufacturer Raytheon.