He basically acknowledged it directly to Dr Bashir in their final conversation. And in the episode you see even the Romulan operative that's working for Starfleet intelligence continue the myth that Section 31 doesn't exist, when we the audience all know it does.During the DS9 era, to my memory, they seemed to have various upper brass members complicit with S31, but I don't remember them ever acknowledging them as a legitimate organization.
Memorya α's article on Section 31:
And section 31 isn't akin to the US CIA per se. It's more akin to the US NSA, which yes is known publicly now, but whose existence was denied for decades in US Government circles.