It is not explicitly shown because I think that would have removed the shock of the action. But remember that Michael, Tom, Al and Rocco are all in the same room discussing business when Michael strikes out at Tom and says "...Are you gonna come along with me on these things I need to do or what" just after Tom has said "Michael, you've won, do you need to kill everyone?". I think Fredo is an unspoken subtext between the two brothers.

So I don't necessarily think Tom was in the room when Michael gave Neri an explicit order but then again why would Neri need one at that point. Michael had already told him that "nothing was to happen to Fredo as long as his mother was alive".

Tom is as good as anyone at picking up vibes so I think he knew Fredo was not long for this world.