Board Thread:Theories and Speculation/@comment-3001903-20161022035220/@comment-734582-20161022095416

Caseather wrote: So why couldn't he get Fugaku's? Because he'd have to enter Konoha to get the flesh which he can't get to. Others died either recently (asuma) or outside Konoha (dan) so there was probably more success in getting DNA.

Also keep in mind that Kabuto only had a few months at best to collect more DNA. Similar threads regarding e.g. Jiraiya popped up and the conclusion was that he probably didn't have enough time.