Bavarian police shot dead the teenager after he wounded four people from Hong Kong on the train and injured a local resident while fleeing. German Interior Minister Thomas de Maiziere has said investigations suggested he was a "lone wolf" who had been spurred into action by Islamic State propaganda.
Der Spiegel said it was likely he used the same axe to try to destroy his phone records.
Citing security sources, the magazine said investigators had been able to attribute two Facebook profiles to the attacker and the information on those filled several thousand pages.
Interior Ministry spokesman Tobias Plate said on Friday the youth arrived in Germany via Austria on June 29, 2015. Police took him into custody in a car park near the border that day because he did not have a passport.
Plate said a comparison of his fingerprints in databases at that time showed he was not known to police back then.
The young man was initially thought to be Afghan but de Maiziere said on Wednesday there were indications he was from Pakistan.
Plate said the man had not yet been interviewed as required by the asylum process, which would have allowed authorities to check his accent and test local knowledge of places in the country he claimed to have come from.
A police search of his home found a hand-written report in Pashto, a language spoken on both sides of the Afghan-Pakistan border.