"Low confidence" here is one of three labels ("low", "moderate", and "high") used to describe both quality and quantity of information behind claims. Government intelligence reports address claims and events using a spectrum of likelihoods and probabilities depending on the strength of supporting information for claims.

Per the United States Office of the Director of National Intelligence (ODNI) which coordinates 18 intelligence community (IC) agencies:

"A low confidence level generally indicates that the information used in the analysis is scant, questionable, fragmented, or that solid analytical conclusions cannot be inferred from the information, or that the IC has significant concerns or problems with the information sources." (page 60, 2011 report)

Essentially, this means the Department of Energy's assessment of the lab leak theory came together with questionable information, thereby any definitive conclusion cannot be drawn, because its evidentiary basis has some essential deficiency or flaw.

Interestingly, "most likely" by definition actually hurts the agency's claim, given its literal meaning necessitates the claim simply has the highest likelihood based on its statistical probability, but is not the only possible (defined by positive [non-zero] probability) cause.