Whitehall sources have revealed that British intelligence officers successfully sabotaged the launch of the first English language website set up by an al-Qaida affiliate.

The officers, understood to be based at Government Communications Headquarters (GCHQ) in Cheltenham, attacked an online jihadist magazine in English called Inspire, devised by supporters of al-Qaida in the Arabian Peninsula.

A pdf file containing fairy cake recipes was inserted into Inspire to garble most of the 67 pages of the online magazine, including instructions on how to "Make a Bomb in the Kitchen of Your Mom".

Though the authenticity of claims made about Inspire have been questioned, British security and intelligence sources say they believe the magazine, and the bomb-making instructions, were genuine.

The sabotage took place a year ago, following a dispute between agencies in the US about who should take on the role of attacking the Inspire website.

Publicising the achievement amounted to little more than a propaganda exercise – "just to let them know", as one British official put it on Thursday.

The head of the US Cyber Command, General Keith Alexander, said blocking the magazine was a legitimate counter-terrorism target and would help protect American troops overseas, according to the Washington Post.

The CIA argued that such an attack would expose sources and intelligence methods and that it amounted to covert action rather than a traditional military one and was therefore its responsibility.

The CIA won the argument and declined to go ahead with the attack on Inspire, the newspaper said.

British security and intelligence agencies, including MI5 (which was not responsible for the attack on Inspire), have made it clear they are deeply concerned about the influence of extreme Islamist and jihadist websites.

But such "website wars" are just the surface of a much bigger threat, British officials say. A much more serious worry surrounds cyber-attacks on government agencies and officials in sensitive jobs.

As US government agencies argue about who should take command – and the Pentagon is fighting back against the CIA – British officials say the UK government is grappling with how to cope with the growing threat.

GCHQ, staffed by encoders and eavesdroppers, has the expertise to defend British agencies and attack hostile ones.

The Ministry of Defence, supported by a new Cyber Operations Group, has a clear interest. So does the Department for Business, Innovation and Skills because private industry must be intimately involved in the battle against cyber-attacks despite potential disputes about competition and intellectual property rights, officials say.

British officials said different government agencies and departments would conduct their cyber operations separately and would be co-ordinated by the Office of Cyber Security and Information Assurance in the Cabinet Office in the heart of Whitehall.

Lieutenant General Rhett Hernandez, head of the US army's cyber command, told a land warfare conference in London on Thursday, organised by the Royal United Services Institute, that a "world-class cyber warrior force" was being built up.

US state department co-ordinator for cyber issues, Christopher Painter, said on Wednesday that America faced potential threats in cyberspace from freelance hackers, militants and potentially rival states.

Diplomacy and policy were only just beginning to catch up with technology, he said. "Cyber-security is now a policy imperative," he told Reuters news agency.

Earlier this week, his employer, the US department of defence, announced it was rewriting its military rule book to make cyber-attacks a possible act of war.

A US official was quoted as saying: "If you shut down our power grid, maybe we will put a missile down one of your smokestacks."

British and US defence and security officials made plain on Thursday that the central problem was how to identify cyber-attackers.