Petraeus, the architect of the current US strategy in Afghanistan, is expected as CIA director to embrace the campaign of drone strikes in Pakistan, a nominally covert CIA operation that has fueled anti-American sentiment but put heavy pressure on militant safe havens.
Continuing or stepping up drone attacks is likely to further strain relations between the CIA and Pakistan's Inter-Services Intelligence directorate (ISI) and, according to some experts, possibly exacerbate the awkward personal chemistry between Petraeus and top Pakistani officials.
Petraeus, nominated by President Barack Obama on Thursday to replace CIA director Leon Panetta, has a reputation for brainpower and political savvy, which he used to help salvage the US campaign in Iraq. Petraeus is not expected to take up his new post until September.
Relations with ISI
Because he helped to craft US policy and has publicly defended it against critics, some officials wonder how open Petraeus will be in his new role to critiquing his own work.
They wonder if he will faithfully represent to the White House a CIA view of Afghanistan and Pakistan that is more pessimistic than that of Pentagon brass. Paul Pillar, formerly the CIA's top analyst on the region, said future CIA assessments of Afghanistan will cover developments since Petraeus' departure as US commander.
But Pillar noted "any such assessments inevitably would reflect well or poorly on the military strategy that had been pursued there for several years. Petraeus would continue to have a strong vested interest in how that strategy is perceived."
Besides Afghanistan, perhaps the biggest issue on Petraeus's agenda at the CIA will be the agency's relations with Pakistan's ISI, which over the last six months have suffered a series of grave setbacks. "I think it is going to be a very strained and difficult relationship," said Bruce Riedel, a former adviser to President Barack Obama on Afghanistan and Pakistan.
Riedel characterised the relationship between Petraeus and Pakistani leaders as "mutual distrust." Petraeus' relationship with Pakistan's military chief, General Ashfaq Kayani, is publicly perceived to be less than friendly and has become a topic of discussion on Pakistani TV talk shows.
Kayani last month issued a rare public condemnation of a US missile strike in a Pakistani region near the Afghan border that killed more than 40 tribesmen.
Last week, he said the drone strikes undermined Pakistan's own war on militants. Still, US officials told Reuters the drone program would move ahead regardless of Pakistani objections.
As commander in Afghanistan, Petraeus increased the use of air strikes but also took steps to limit civilian casualties. But in a move unlikely to win him new friends in Islamabad, Petraeus as CIA chief is expected to renew US demands that the ISI sever ties with anti-Western insurgents attacking American forces in Afghanistan - accusations reflecting continuing deep mistrust between uneasy allies.
Controversial Afghanistan policy
Current and former US national security officials say there is concern among some veteran spies about Petraeus' advocacy of controversial military policies, particularly his expansion of counterinsurgency in Afghanistan.
One of the CIA's principal roles, the officials say, is to provide the president and his top advisors with objective, non-politicized advice about world events and the effectiveness of American foreign policy in responding them. But in his role as US military commander in Afghanistan, Petraeus has been a developer of the counterinsurgency strategy whose results are incomplete as the Obama administration plans to begin a withdrawal of US soldiers this summer.
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