"Some 3,000 ANA soldiers have fled the army," ministry spokesman General Mohammad Zahir Azimi said.
"The defense ministry has announced that they have to come back and join the army otherwise they will have to pay for all the expenses spent on their training."
The desertions are a serious blow to the nascent ANA which, according to Zahir Azimi, numbers around 10,000 troops. However, international observers believe the real strength of the ANA is closer to 7,000.
Even though it is forecast to grow to be about 70,000-strong, the ANA's numbers are small in comparison to the 100,000 armed militia currently being disarmed and demobilised by government authorities.
Tough training, low wages and factional links to the private militias which still control wide swathes of the country outside Kabul are believed to be behind the mass exodus from the ANA.
It is not known how much money has been spent on the deserters but recruits receive 50 US dollars a month during training and a minimum wage of 70 dollars per month after that.
In addition to their imported uniforms and tuition, soldiers receive a seven dollar a day food allowance and 60 dollars a month if they go on exercises outside the capital Kabul.
The ANA was formed in May 2002 after the ousting of the Islamic fundamentalist Taliban regime by US-led forces.
The ANA accepts volunteers and initially local militia commanders and warlords were instructed to force some of their troops to join the national army, although this practice has stopped.
"The militia commanders introduced the weak and lazy ones (into the ANA), not the active fighters, and they couldn't bear the tough training," Zahir Azimi said.
"The salary they were paid was less than what they could make in a month doing other things so they left.
"Now it is totally volunteer soldiers and that is why in the last several months we haven't had any escapes."
Afghanistan has endured almost three decades of war. The 1992-1996 civil war destroyed all government institutions, including the national army.
After the collapse of the Taliban regime in 2001, the Bonn agreements laid out plans for a national army and a police force to gather weapons and disarm militia.
The formation of the ANA was supervised by the US army but with the assistance of Britain, New Zealand and France. Germany, Bulgaria, Romania, Canada, South Korea and Mongolia also supplied technical assistance.
Disarming private militias is one of the priorities for President Hamid Karzai as he attempts to extend the authority of his government to the provinces, which have been troubled by factional fighting and rights abuses by commanders.