Hundreds of soldiers have deserted the Afghan National Army complaining of poor conditions and fierce resistance from the Taleban, US officials say.
It is a blow to the Afghan government which wants to increase the size of the force so the numbers of international troops in the country can be reduced.
The corps affected is the first to be deployed in the field.
Officials say another reason for men going absent is the difficulty they experience in dealing with their pay.
The 205th Corps of the Afghan National Army is based around the city of Kandahar.
The south of Afghanistan has seen some of the fiercest fighting against remnants of the Taleban and their al-Qaeda allies.
Members of the corps are in combat most days.
A US military spokesman told the BBC that around 300 men have deserted.
That is one in 12 of the entire force.
Soldiers are paid around $75 a month - a good wage in Afghanistan - but the absence of a banking system prevents them from sending money to their families.
The news comes as American troops take more casualties.
On Wednesday two US soldiers were killed and eight others wounded in a rocket attack near the border with Pakistan.
The Afghan government's long term plan is for the numbers of international troops in the country to be reduced and for Afghanistan's own army to shoulder more of the burden of the fighting.
To do that numbers will need to be nearly tripled to around 70,000 by 2007.