The US government was accused of hiding the truth about its drone programme after leaked intelligence files revealed that it was targeting unidentified militants who posed no immediate threat to the United States.

Despite President Barack Obama’s public promise that the CIA’s armed Predators and Reapers were only firing on those suspected of plotting against America, top-secret documents show that in one year alone almost half of those killed were simply listed as “unknown extremists”.

The documents, obtained by US news agency McClatchy, also reveal Pakistan’s intelligence agency was co-operating with the US at the same time as its government was condemning drone strikes on its soil.

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“There is now mounting evidence that the Obama administration is misleading the American public – and the world at large – about the drone war it is waging in Pakistan,” said Jennifer Gibson, a lawyer working with the British human rights charity Reprieve.

“The reports show a significant number of the strikes have nothing to do with al-Qa’ida. Instead, they may have been a quid pro quo exchange between two countries’ spy agencies. The result is that the US often doesn’t know who it is killing.”

The US has come under increasing international pressure to open up its decision-making process to scrutiny following claims that the drone programme has killed hundreds of civilians among an estimated death toll of 2,500, predominantly in Pakistan and Yemen. Preparations are in place to transfer more control of the programme from the CIA to the Pentagon, in a move said to herald greater transparency.

The US intelligence reports leaked to McClatchy covered, its reporters said, most of the drone strikes in Pakistan during 2006 to 2008 as well as 2010 to 2011. Most of the attacks targeted al-Qa’ida but many were aimed at the Haqqani network and factions of the Pakistani Taliban.

At least 265 of the 482 people killed by the CIA programme in the 12 months up to September 2011 were listed as Afghan, Pakistani or “unknown extremists”.

This contrasts sharply with US administration’s claim that drones are only used to target “senior operational leaders” in al-Qa’ida, those involved in the 11 September 2001 attacks or individuals plotting imminent attacks on the US.

Last night a spokesman for the US Department of Defence said neither they nor the CIA commented on intelligence matters.