As part of a shakeup of his national-security team, President Barack Obama is expected to nominate General David Petraeus to direct the CIA. Petraeus currently commands American and ISAF forces in Afghanistan but acquired fame as the general who led the “surge” in Iraq in 2007.

Petraeus would replace Leon Panetta who is set to succeed Robert Gates as defense secretary this summer. Marine Corps Lieutenant General John Allen would move from his post as deputy commander of US Central Command in Florida to take over the Afghan campaign.

The general’s move to intelligence is far from expected as defense analysts considered him a potential next chairman of the Joint Chiefs of Staff. Admiral Michael Mullen is expected to retire from that position in October.

The staffing changes come at a pivotal moment for the war in Afghanistan where Petraeus is supposed to start withdrawing troops after the summer. Because the country is bracing for a violent season, the general hasn’t made his recommendations for a drawdown in troop levels yet. Close to 100,000 American soldiers are stationed in Afghanistan and Petraeus likes to keep as many as possible for as long as possible.

According to the administration’s latest assessment of the war, the “surge” in Afghanistan, which saw 30,000 additional American troops deployed last year, has had considerable success, particularly in the Pashtun dominated south, although gains made there remain fragile and reversible.

American combat operations have mounted in number and intensity under Petraeus’ command. Night raids have significantly increased. Airstrikes nearly doubled. But in part because the Taliban have sanctuaries across the border in Pakistan, they continue to be able to menace the population of areas and towns that are won by the coalition. Moreover, Afghanistan’s civil administration is often ineffective and corrupt, undermining a counterinsurgency effort that is designed to win the “hearts and minds” of the populace.

Taking Petraeus out of Afghanistan at such a critical juncture in the war may seem an odd decision and it has already been criticized by some conservatives. Petraeus has only been at the job since the summer of last year when he replaced General Stanley McChrystal. Although that was supposed to be a mere “change in personnel, not a change in policy,” according to Obama, the Iraq veteran worked to improve relations with Afghan President Hamid Karzai and tried to convince the Pakistanis to crush the militants that are operating along their western frontier.

Both Karzai and Pakistan have staked a lot on America’s commitment to Afghanistan. After the terrorists attacks of September 11, Pakistani President Pervez Musharraf provided more support for the war effort than any Western ally. He allowed the United States to gather intelligence on his soil and execute military strikes against suspected insurgent strongholds. Islamabad helped destroy he Taliban though it couldn’t have had an Afghan regime more compatible with Pakistan’s national interests.

Pakistan is now itself on the brink of civil war. American officials continue to urge it to step up its campaign against the Taliban in North Waziristan and the tribal area west of Peshawar but the Pakistanis are reluctant, arguing that they should first consolidate gains in South Waziristan and Swat before opening another front. Instead of expanding its efforts, the Pakistani military has demanded an end to American drone strikes in the border region which are deeply unpopular among the local population.

Karzai’s government is under mounting pressure from the Taliban and its sympathizers and has suggested that it might have to reach some sort of accommodation if American troops to pull out. Petraeus’ departure would make it all the more difficult for the Obama Administration to convince its allies in Islamabad and Kabul that it is not quickly bolting for the exit despite waning support for the war at home.