The 33-year-old is still working his way back to fitness after suffering an ankle injury in May which ruled him out of last month's World Cup, but German magazine Kicker says Löw believes he is still short of match fitness.
The coach will name his squad on Friday for the qualifiers against Belgium and Azerbaijan and if Ballack is not selected, Bayern Munich defender Philipp Lahm is likely to retain the captaincy having led Germany to third at the World Cup.
Löw was in Dortmund last Sunday to see Ballack make his first appearance back in the Bundesliga after four years in the Premier League with Chelsea as his side Leverkusen beat Dortmund.
The national coach has always said he will only select players in peak condition and with Germany facing Belgium in Brussels on September 3 and Azerbaijan in Cologne on September 7, Ballack is out of time, claims Kicker.
After his injury, Ballack only returned to training at the start of August and has played only a Bundesliga and Europa League match.
He will miss Thursday's return leg clash against Ukrainians Simferopol in the Europa League with Bayer holding a 3-0 lead as he continues to work on his fitness.