Marine general Dunford will likely be the last commander of the United States' longest war, tasked with bringing forces home after more than 11 years and overseeing the transfer of Afghan security duties to local forces.
Despite the persistence of the Taliban's bloody insurgency against President Hamid Karzai's government and NATO forces, Allen, who leaves to become the alliance's supreme commander in Europe, said the coalition was "on the road to winning".
Dunford, a Marine general like Allen who earned the nickname "Fighting Joe" for his leadership in Iraq, took command of the International Security Assistance Force (ISAF) in a ceremony at the group's headquarters in Kabul amid tight security.
In an interview with the BBC, Allen said it was difficult to "put a dot on the calendar" to mark victory in a counter-insurgency campaign, but insisted the NATO effort was moving in the right direction.
"I think we have gone a long way to setting the conditions for what, generally, usually, is the defining factor in winning a counter-insurgency -- to set the conditions for governance, to set the conditions for economic opportunity.... I think we are on the road to winning," he told the broadcaster.
Allen was the fourth ISAF commander under US President Barack Obama, and his 19-month tenure was punctuated by a series of crises, from the accidental burning of Korans at a US base to images of US soldiers urinating on the bodies of Taliban fighters.
There was also controversy about Allen's own conduct after he became embroiled in the sex scandal that brought down David Petraeus, the CIA director -- and Allen's predecessor as ISAF chief.
The Pentagon exonerated Allen last month over emails he sent to a woman tied to the Petraeus affair, which defence officials had said were potentially "inappropriate".
But perhaps the most difficult aspect of Allen's time at the head of ISAF has been the surge in so-called "green on blue" insider attacks, in which Afghan security forces turn their weapons on their NATO allies.
The attacks have risen sharply in the last year, with more than 60 foreign soldiers killed in 2012, breeding mistrust between Afghan and NATO troops and threatening to derail their mission to train local forces to take over security duties.
Afghan soldiers and police are taking on responsibility for battling the militants from NATO's 100,000 troops who will leave by the end of next year --more than a decade after a US-led invasion brought down the Taliban regime.
It is still unclear how many troops Washington will leave behind in Afghanistan beyond 2014. Reports last month citing the US Defense Department suggested that between 3,000 and 9,000 troops would stay to focus on preventing Al-Qaeda, which was sheltered by the 1996-2001 Taliban regime, from regaining a foothold in Afghanistan.
The number of foreign soldiers battling the Taliban-led insurgency has already fallen to 100,000 from about 150,000. Of those, 66,000 are US troops, down from a maximum of about 100,000.
AFP
