De Hoop Scheffer said the 8,500-strong International Security Assistance Force (ISAF) force of NATO troops and the 16,000 soldiers under the Operation Enduring Freedom banner could share commanders while maintaining their separate tasks.
"We need more synergy and more cooperation between ISAF and Operation Enduring Freedom.
"I don't know about them being completely merged, but I can imagine a double-headed command structure with two different missions," De Hoop Scheffer said after a meeting with German Defence Minister Peter Struck.
The NATO chief said the issue would be on the agenda of an informal meeting of NATO defence ministers in Berlin on September 13-14.
Struck returned on Monday from a visit to Afghanistan to check on the progress of German troops serving in the 37-nation ISAF force which was set up in December 2001 after the defeat of the Taliban regime.
While ISAF's duties are restricted to peacekeeping and reconstruction, Operation Enduring Freedom is hunting remnants of the Taliban and their Al-Qaeda allies in southern and eastern Afghanistan.