The entire print run of a highly critical and embarrassing account of Britain's role in southern Afghanistan has been bought and pulped by the Ministry of Defence at a cost of more than £150,000.

A new edition, with some 50 words taken out, will be published this week despite continued opposition from within the ministry, officials said on Monday.

Dead Men Risen: The Welsh Guards and the Real Story of Britain's War in Afghanistan, by Toby Harnden, says Lieutenant Colonel Rupert Thorneloe, the most senior soldier killed in war since the Falklands, lacked adequate equipment – including anti-IED protection – and sufficient manpower to do the job his soldiers were asked to do.

Thorneloe, a family friend of the author and commander of 1st Welsh Guards, was killed on 1 July 2009. The book draws from memos he sent to his commanders, including criticism of the British strategy.

The Guardian has obtained a copy of the book, which includes accounts of how civilians were killed by British forces. It describes a farmer being killed by a Javelin missile at night, how seven civilians, including six children, were killed by a 500lb bomb – an incident described by the Guardian from classified US material passed to WikiLeaks – and how eight civilians, including five children, were killed by a 500lb bomb fired by a French Mirage plane called in by British troops.

The book describes how in the summer of 2009 a British officer was mentoring Afghan troops who captured a six-man Taliban IED team. He later asked an Afghan sergeant major to see the prisoners so they could be tested for explosive residue, and charged, and processed.

The Afghan soldiers described how three of the prisoners were strangled to death as the others watched. The soldiers said the remaining three were shot in both kneecaps and ordered to crawl back to their villages to tell people what would happen to them if they laid IEDs.

British military police are understood to have carried out an inquiry into the incident but concluded there was insufficient evidence to take the matter further.

Harnden said the British officer, Major Rob Gallimore, had backed up the description of the incident involving the captured Afghans.

An MoD spokesman said: "The MoD has bought the entire first print run of the book. This action was taken because at a late stage the text of the book was found to contain information that could damage national security and put at risk the lives of members of the armed forces."

He added: "Faced with the stark choice between compromising the security of members of the armed forces and their families and making payment to the publisher for amendments to a book which had already been printed, MoD had little option but to negotiate a settlement."