I believe this is mentioned in the second or first databook, but I don't believe it extends to every ninjutsu in Konoha, as Hiruzen had retired from being a ninja by the time Minato became Hokage, and also I am not quite sure what they mean by counter.
For instance a counter to one jutsu could be just dodging it, so they need to explain that more. If they are trying to imply that he has a ninjutsu for every other ninjutsu in Konoha that would nullify/counter/ overpower the other one, then I will respectfully call BS.