US General John Allen will take over as NATO supreme commander and be replaced as head of alliance forces in Afghanistan by Joseph Dunford, currently US Marine Corps deputy commander, US Defense Secretary Leon Panetta said Wednesday.

Allen, who succeeds Admiral James Stavridis in a post traditionally held by a US officer, led the NATO campaign in Afghanistan from July 2011.

Panetta made the announcement after a meeting of NATO defence ministers in Brussels. Both nominations by President Barack Obama are subject to US Senate confirmation.

"For more than a year, General Allen has served with distinction as the commander of US forces and NATO's International Security Assistance Force (ISAF) in Afghanistan, seeing us through a critical period in our military efforts and in Afghanistan's transition," a statement from Obama said.

"I have personally relied on his counsel and am grateful for his devotion to our national security and to the safety of the men and women with whom he serves," Obama said.

"Under General Allen's command, we have made important progress towards our core goal of defeating Al-Qaeda and ensuring they can never return to a sovereign Afghanistan."

Allen played a key role in countering the Iraq insurgency during 2006-08 and took over from General David Petraeus in Afghanistan to oversee a surge in US troop levels to force back the Taliban who appeared to be making ground.

"During his tenure in Afghanistan, General Allen established his credibility with our NATO allies and ISAF partners as a strong and effective military leader," Obama added.

In Afghanistan, Allen commanded a coalition force from 50 different countries, giving him the experience to deal with the often sensitive and conflicting wishes of NATO's 28 member states and 22 partners.

In Iraq, Allen pushed alliances with local Sunni tribes to tame an insurgency which at one stage looked as if it could not be brought under control.

Patraeus, his then commander in Iraq, later expanded the tactic to the entire country.

Dunford will assume command of 68,000 US troops who make up the bulk of the coalition force of some 100,000 as the Afghan army takes on increasing responsibility for security and NATO ends its combat mission in 2014.