A US military plan to survey refugee camps and aid agencies on the Pakistan-Afghanistan border, possibly to obtain targeting information for air strikes, sparked alarm among diplomats in Islamabad.

In mid 2008 the US defence department special operations command requested US embassies in Kabul and Islamabad to provide information on camps housing Afghan refugees or civilians displaced by fighting with the Taliban.

"They have requested information on camp names and locations, camp status, number of IDS/refugees and ethnic breakdown, and NGO/humanitarian relief organisations working in the camps," read a cable from the Islamabad embassy.

The defence attache's office was instructed to "reach out" to the UNHCR (the UN refugee agency), USAid and the state department.

The information was requested in response to the special operations command – which oversees secret US military missions – "regarding [internally displaced people] IDP/refugee camps and NGO activity". The purpose of the request was not clear, the cable noted cautiously.

"Some emails have suggested that agencies intend to use the data for targeting purposes; others indicate it would be used for 'no strike' purposes."

The diplomats seemed alarmed by the idea. "We are concerned about providing information gained from humanitarian organisations to military personnel, especially for reasons that remain unclear. Particularly worrisome, this does not seem to us a very efficient way to gather accurate information," the cable said.

The embassy curtly noted that such requests should be directed to the CIA station chiefs in Kabul and Islamabad and the local representatives of the director of national intelligence. The diplomats' sensitivity was understandable. The request came three months after US navy Seals carried out a cross-border raid on a militant base in South Waziristan that drew a furious response from Pakistani officials.

The most likely target of any US strikes against refugee camps would be in the western province of Balochistan, home to the Taliban leadership council, the Quetta Shura. The cables show US and Pakistani officials believe the Taliban use such camps to arm, train and recruit fighters.

"The only parts of Balochistan where there are Pakistani Taliban are in the province's Afghan refugee camps, which we are planning to shut down," President Pervez Musharraf told Senator John McCain in April 2007.

But despite repeated promises, the Pakistani government has failed to close the biggest and most notorious Balochistan camps, such as Girdi Jungle and Jungle Pir Alizai. Some embassy cables claimed the army was playing a "double game", allowing the Afghan Taliban to operate in Balochistan in order to influence the outcome of the war in Afghanistan.

Pakistani officials repeatedly deny this. "Let me tell you," Musharraf emphasised to McCain, "[Taliban leader Mullah] Omar would be mad to be in Quetta – he has too many troops to command in southern Afghanistan to make it feasible."

Some Pakistani officers denied a problem existed at all. In a "flag meeting" between Nato and Pakistani officers on the border at Kandahar in October 2009, the Pakistani commander called the Quetta Shura an "unsubstantiated fabrication". The Americans had "fallen victim to rumours", Brigadier Sajjad said, adding that Taliban infiltration into Afghanistan from Pakistan was negligible and that "if there were any Taliban leaders around they would know about them".

The past year has seen speculation that the CIA may expand its drone strike campaign to include targets in Balochistan. But they remain confined to the tribal belt, further north along the border.

The cables do not record what happened to the 2008 request for information on the border refugee camps..