They are one and the same thing. Are you suggesting that Pakistani intelligence agencies are not Part of Pakistan?
Well I can't say what SM Krishna is suggesting, but I think it would be fair to say that intelligence agencies (or parts thereof ) have acted outside civilian control most of the time sometimes even controlling the political situation itself. ISI still maintains contacts with Taliban (both the Pakistani and Afghan version) as was claimed by none other than Kiyani himself, now what is the level of co-operation or level of control over them, we can only speculate, and I don't want to indulge in that.