John Henry Browne said there was “no forensic evidence” against Staff Sgt Robert Bales and “no confession”.
He also dismissed reports suggesting Sgt Bales, 38, was having financial troubles as irrelevant to the case.
Sgt Bales is being held a military detention centre awaiting charges, which are expected this week.
The killings have undermined US relations with Kabul and led to calls for Nato to speed up their planned withdrawal of troops from Afghanistan.
After meeting with Sgt Bales at a US army base in Kansas, Mr Browne told reporters: “We’ve all heard the allegations. I don’t know that the government has proved much.”
Sgt Bales is the only known suspect in the killings – despite repeated Afghan assertions that more than one American was involved.
Mr Browne said he now plans to travel to Afghanistan to gather his own evidence.
Sgt Bales and his wife were reportedly having trouble making their mortgage payments
“Sure, there are financial problems. I have financial problems. Ninety-nine percent of America has financial problems,” he said.
“You don’t go kill women and children because you have financial problems.”
The Pentagon has previously said that Sgt Bales could face charges that carry a possible death penalty.
Such a trial could take years, contrasting with Afghan demands for swift and decisive justice.