US General David Petraeus admitted Wednesday there was no option but to work on troubled relations with Pakistan, days after standing down from his job at the helm of coalition forces in Afghanistan.

Speaking in Paris on his way to his new job as CIA chief, the most celebrated military leader of his generation said Afghanistan's neighbour wanted to eliminate Al-Qaeda and Taliban militants but was struggling.

"They'll be the first to say that there are limits to how much they can do," said the man who headed the United States' longest-running war for the last year, with less territory controlled by militants today but civilian deaths up.

"They have a lot of short sticks in hornets nests right now and they have to consolidate some of those gains."

Petraeus said Pakistani anti-militant operations have been impressive but they "clearly need further effort to deal with some of the other elements, like the Qaeda network in North Waziristan and the Taliban in Baluchistan".

"This relationship is in a difficult stage," Petraeus said, blaming WikiLeaks revelations, the arrest of CIA agent Raymond Davis as well as the killing by US forces of Al-Qaeda kingpin Osama Bin Laden in Pakistan in May.

He said it was believable that Pakistani intelligence did not know that Bin Laden was hiding out in Abbottobad, home to much of the Pakistani military establishment, when he was killed there.

"It is credible to me that they did not know. We received no intelligence whatsoever to indicate that there was any awareness that he was there."

But while "we see the Bin Laden raid as an extraordinary success, intelligence together with military forces, Pakistan sees it as an affront to their national sovereignty, we've got to work our way through this".

"We know what happens when we walk away from Pakistan and Afghanistan, we've literally seen the movie before, it's called 'Charlie Wilson's War' (about covert US support for anti-Soviet Afghan fighters) and indeed that is not in my view a good option.

"However difficult the relationship may be it's one we need to continue to work, it's one where we need to recognise what our Pakistani partners have done, they've sacrificed several thousand soldiers and police and their civilians have suffered substantial levels of violence."

Petraeus oversaw a surge of tens of thousands of troops into Afghanistan in a last-ditch bid to reverse a nearly 10-year Taliban insurgency and repeat the success of a similar surge he masterminded in Iraq.

But with Taliban leaders not currently wanting to join the political process in Afghanistan, Petraeus said US and Afghan authorities should work on what he said was militants' creeping dissatisfaction with their commanders.

"In Iraq what we achieved was the reintegration of reconcilable elements, if you can get 20,000 reintegrees, the senior leaders become immaterial."

He accused senior Taliban commanders of "leading from luxury" by issuing orders from Pakistan to fight in Afghanistan and that footsoldiers were unhappy with his.

"Those who are doing the fighting are gradually catching on to this, there is a degree of gradually growing resentment that the senior leaders never set foot in Afghanistan rather they send the mid-level leaders and fighters in."

"If we take them away and reintegrate them you will have achieved something very significant and that could help the process considerably."

Despite wanting to improve relations with Pakistan, Petraeus is likely in his new job as CIA chief, which he starts in September, to escalate the United States' covert drone war against militants in Pakistan.

He said that ideally when dealing with nations where militants are hiding out you provide intelligence, alternatively you help their ability to deal with it themselves and then you "help them by actually doing it ourselves".

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