A new Israeli report defending the military's conduct in the Gaza war was challenged tonight after evidence emerged apparently contradicting one of its key findings.

Israel submitted a 46-page report to the UN on Friday saying its forces abided by international law throughout the three-week war last year. It was meant to avert the threat of international prosecutions and to challenge a highly critical UN inquiry by South African judge Richard Goldstone, which accused both Israel and Hamas of "grave breaches" of the fourth Geneva convention, war crimes and possible crimes against humanity.

The Israeli report looked in detail at a handful of incidents, including the attack on the al-Badr flour mill in northern Gaza, which was severely damaged.

The UN mine action team, which handles ordnance disposal in Gaza, has told the Guardian that the remains of a 500-pound Mk82 aircraft-dropped bomb were found in the ruins of the mill last January. Photographs of the front half of the bomb have been obtained by the Guardian.

This evidence directly contradicts the finding of the Israeli report, which challenged allegations that the building was deliberately targeted and specifically stated there was no evidence of an air strike. Goldstone, however, used the account of the air strike as a sign that Israel's attack on the mill was not mere collateral damage, but precisely targeted and a possible war crime.

The flour mill attack was not the most serious incident of the war: although nearly 1,400 Palestinians and 13 Israelis were killed in just three weeks, no one died at the mill. However, because it was a civilian building producing food – the only operational mill in Gaza – the incident received particular criticism from Goldstone, who concluded that the building was hit by an air strike, the attacks were "intentional and precise", and they were "carried out for the purpose of denying sustenance to the civilian population". He added that the attacks violated the fourth Geneva convention and customary international law and may constitute a war crime.

In its defence, the Israeli report admitted the building had been hit by tank shells but said it was a "legitimate military target" because there were Hamas fighters "in the vicinity of the flour mill". It said the mill was "not a pre-planned target" and specifically denied it was hit by an air strike.

"The military advocate general did not find any evidence to support the assertion that the mill was attacked from the air using precise munitions, as alleged in the human rights council fact-finding report," it said. The military advocate general "found no reason" to order a criminal investigation.

But the Guardian visited the mill days after the war last year and on the first floor of the building saw what appeared to be the remains of an aircraft-dropped bomb in the burnt-out milling machinery.

The UN mine action team said it identified an aircraft-dropped bomb at the mill on 25 January last year and removed it on 11 February. "Item located was the front half of a Mk82 aircraft bomb with 273M fuse," according to the team. "The remains of the bomb were found on an upper floor in a narrow walkway between burnt-out machinery and an outside wall." The bomb was made safe by a technical field manager and removed.

The team also provided two photographs of what it said were the bomb remains, marked with the date and time it was identified: "25 Jan, 14:38". The team did not do a damage assessment of the building to see what other ordnance hit because that was not its task.

Asked to explain the new evidence today, the Israeli military referred the Guardian to an Israeli foreign ministry statement that summarises last week's report and states that the military is "committed to full compliance" with the law of armed conflict and to investigating any alleged violations.

As well as the heavy death toll, the Gaza war damaged a large amount of civilian infrastructure: more than 21,000 buildings and apartments were wholly or partly destroyed, including more than 200 major factories.

The al-Badr flour mill was the largest mill in the strip, with production lines spread over five floors – each of which were hit. Gaza's largest concrete factory, at a different site a few miles away, was also destroyed, as were several large food processing plants.

Goldstone said the nature of the attack on the flour mill "suggests that the intention was to disable its productive capacity" and said there was no plausible justification for the extensive damage. "It thus appears that the only purpose was to put an end to the production of flour in the Gaza Strip," his report said. It is not clear why Goldstone did not use evidence from the UN team in his report.

Rashad Hamada, one of two brothers who owns the mill, gave evidence at a public hearing in Gaza last June and said the mill was hit by an air strike. He said the ­factory twice received phone calls from the Israeli military telling them to evacuate the building in the days before the strike, but the factory was not used by Hamas or other Palestinian fighters.

Both Hamada brothers possess hard-to-obtain businessmen's permits to enter Israel and were therefore regarded as ­credible ­witnesses by the Goldstone team.

"What happened at the mill is total destruction of the whole production line of the factory," Hamada said. He ­estimated his losses due to the destruction were $2.5m (£1.7m) and said he believed that the mill had been targeted because it was working.

Four other flour mills in Gaza that were not operational were not targeted, he said. "As for the targeting, it is because [it was] a flour mill that is ­working," he said.