"Four of them are no longer in the army. We will take the appropriate steps against the other two," he told ZDF public television.
Deutschlandfunk radio said one of the men had admitted playing and posing with a skull while stationed in Afghanistan.
The Bild newspaper had published photographs of German soldiers serving with the NATO-led International Security Assistance Force in Afghanistan showing off the skull like a battle trophy.
In one of the pictures, a soldier mounts the skull on the cablecutter at the front of a patrol vehicle, which bears both the German flag and the acronym for the international force, ISAF.
In another, a soldier in camouflage uniform and a bullet-proof vest poses with the skull next to his exposed penis.
Bild said the photographs were taken outside Kabul in spring 2003.
According to the defence ministry, the men may have taken the skull from a cemetery south of the Afghan capital.
The affair has outraged Germans and the soldiers' conduct has been widely condemned.
German Chancellor Angela Merkel termed the pictures "shocking and disgusting" and promised tough steps against the culprits.
State prosecutors are investigating criminal charges of disturbing the peace of the dead, a crime that carries a prison sentence of up to three years in Germany.
The country is the second biggest contributor of peacekeepers to Afghanistan with some 2,750 troops and holds the command of ISAF in the north.