Earlier this month, Defense Secretary Chuck Hagel reinstated nearly all of the 400,000 of the department's civilian workforce that had been furloughed due to the shutdown.
Days later, Hagel and Pentagon leaders announced it would begin paying out death benefits to the families of service members killed in action, after those payments had also been suspended due to the shutdown.
Payments would be made through the Fisher House Foundation, which provides housing for family members of service members receiving medical care, as the shutdown continues to freeze department coffers.
The Pentagon will reimburse the nonprofit group once the federal government is up and running again, according to Hagel.
But the decision to suspend civilian workers and death benefits, only to reinstate both under near-term legislative fixes, shows the haphazard nature of the Pentagon's reaction to the shutdown fiasco, according to Panetta.
“These decisions have been by the seat of the pants, what’s essential and what’s not essential. I think not enough thought was put into how exactly this would be implemented,” he said Monday.
But Panetta, who also headed up the CIA in Obama's first term, saved his harshest criticism for the administration's decision to furlough more than 70 percent of the civilian workforce in the in the intelligence community.
“Who the hell came up with that?” he asked in response to the intelligence workforce cuts during a breakfast hosted by The Wall Street Journal.
“Everybody could have done a better job, especially on this intelligence stuff,” he added.
Director of National Intelligence James Clapper told Congress that it could be easier for enemies to recruit U.S. spies among the federal employees hit by furloughs.
"This is a dreamland for foreign intelligence service to recruit, particularly as our employees already ... [subjected] to furloughs driven by sequestration, are gonna have even greater financial challenges," he said during an Oct. 2 Senate Judiciary Committee hearing.
"I've been in the intelligence business for about 50 years. I've never seen anything like this," Clapper added during a Senate Judiciary Committee hearing Wednesday.
Clapper said the loss of income from sequestration and the shutdown could make members of the intelligence community more susceptible to bribes.