Less than a week after a US staff sergeant allegedly massacred 16 civilians in Kandahar, American soldiers were banned from bringing guns into a talk by Mr Panetta at a base in Helmand province.
Around 200 troops who had gathered in a tent at Camp Leatherneck were told "something had come to light" and asked abruptly to file outside and lay down their automatic rifles and 9mm pistols.
"Somebody got itchy, that's all I've got to say. Somebody got itchy – we just adjust," said the sergeant who was told to clear the hall of weapons.
Major General Mark Gurganus later said he gave the order because Afghan troops attending the talk were unarmed and he wanted the policy to be consistent for all.
"You've got one of the most important people in the world in the room," he told the New York Times, insisting that the decision was unrelated to Sunday's killings. "This is not a big deal."
However, US troops often remain armed even when their Afghan colleagues have been asked to lay down their weapons and the incident is believed to be the first time they were stripped of guns during an address by their own secretary of defence.
The Ministry of Defence was unable to confirm reports that a small number of British troops had also been asked to put down their weapons.
Mr Panetta told the troops that the massacre of civilians and the resulting Afghan fury would not affect plans to keep US troops in the country until the end of 2014.
"We will be challenged by our enemies, we will be challenged by ourselves, we will be challenged by the hell of war itself," he said.