Claims the US-led coalition and Iraqi forces violated international humanitarian law in the battle to recapture Mosul from Islamic State are “deeply irresponsible”, a senior British commander has said.

Major General Rupert Jones, the deputy commander of the international anti-IS coalition, has slammed the report published by Amnesty International on Tuesday as “disrespectful” to the Iraqi government.

Days after a “total victory” in Mosul was declared by the Iraqi prime minister, the human rights organisation suggested the government and coalition carried out “disproportionate” and “unlawful” attacks in the fight to take back the city.

Amnesty said Iraqi forces and the coalition have killed and injured thousands, and appear to have committed “repeated violations of international humanitarian law”, some of which “may amount to war crimes”.

Pressed on the claims, Gen Jones said the report is “deeply irresponsible and frankly naive”.

“It is riddled with assertion, at no stage did they have the courtesy to engage the coalition to ask what our targeting process is,” he said.

“So to me it is a deeply discredited report and does a great disservice to Amnesty International, but more importantly a great disservice to the Iraqi security forces and to the government of Iraq.

“Firstly the Iraqi security forces have put the safety of civilians as the absolute centrepiece of the liberation of the city over the last nine months – that is beyond question.

“Does that mean there have been no violations? No, of course there have, but whenever those are presented to the government of Iraq, they are taken very, very seriously.

“The second thing would be to say that the coalition in providing support to the Iraqi security forces, we go to extraordinary lengths to ensure that when we strike we only kill the enemy. I would say it is the most sophisticated targeting and strike process in history.”

Gen Jones said it is naive to think a city such as Mosul with a population of 1.75 million could be liberated without any civilian casualties while fighting an enemy that “lacks all humanity”.

“It strikes me as being written by people who simply have no understanding of the brutality of warfare. But we should be absolutely clear who were deliberately killing civilians,” he added.

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“It wasn’t the government of Iraq, it wasn’t the coalition, it was Isis – everybody should be entirely clear what they were doing with the civilians.

“It went way beyond human shields, they were out and out murdering civilians left, right and centre.”

After IS seized control of Iraq’s second biggest city in June 2014, Mosul became a stronghold for the extremist group.

Gen Jones said it is “huge kudos” to Iraqi government forces that they have now liberated the city held by IS for more than three years.

“We should just briefly take stock, it was a nine-month battle – probably the most significant urban battle since the Second World War – and the Iraqi security forces prevailed, with the support of the coalition, and they did so with great style,” he added. “I think the whole world should congratulate them for that.”

But he warned there will still be “pockets which need to be tidied up” within Mosul, and that the recapturing of the city does not mean the end of IS in Iraq – with areas yet to be “cleared”.

“The message to the international community should be this is a hugely decisive blow against IS but don’t think it is the end, it isn’t. There is still hard fighting to follow,” Gen Jones said.

When quizzed about the challenges now facing the Iraqi government and coalition in the wake of Mosul’s liberation, he said the city has got be stabilised following the “huge trauma” of war.

Gen Jones said another issue the Iraqi government needs to address is ensuring that no one feels “disenfranchised”. Whether they be Sunni, Christian or another minority, he said they should feel as though they have a stake in the future of Iraq.

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The UK is just one country that makes up the Global Coalition of 72 members joined together in a commitment to eradicate IS.

With the liberation of Mosul acting as the coalition’s priority until its recapture, Gen Jones said attention has now turned to the Syrian city of Raqqa, the self-proclaimed capital of IS.

Just over a month into that battle, alongside the Syrian Democratic Forces, he said a tough fight can be expected but that forces have made “really good progress” and broken into the city in a number of places.

Stressing that putting a timeline on the operation would be “sheer folly”, he added: “They are making great headway, but we shouldn’t expect it to be quick… it will take a bit of time.”