About 1000 former employees were involved in Sunday’s demonstration which saw protesters shooting out windows and soldiers firing back into the crowd, witnesses and authorities said.
Military officials said the ministry is determined to pay back wages, but does not yet have the finances.
The Hamid Karzai government is almost entirely dependent on foreign aid.
Thousands of employees and former employees are owed months of wages.
Afghanistan has received significant pledges of financial support but little of that has reached the country's coffers.
In a speech last year, President George Bush said the US and 60 other countries had pledged $4.5 billion in aid to Afghanistan over five years at a donors conference in Tokyo and added: "We're currently implementing more than $300 million worth of reconstruction and recovery projects."
Washington spends about $10 billion on Afghanistan annually, but most of that money goes towards supporting the 9000 US troops deployed there.
US Congress authorised $3.3 billion in financial and military assistance to Afghanistan in late 2001 but little of that has been spent.