England left-back Shaw, a summer signing from Southampton, returned late to club training after spending the summer with Roy Hodgson's squad at the World Cup in Brazil.
Shaw trained on his own at FedEx Field in Washington on Monday as Van Gaal oversaw preparations for the friendly clash with Inter Milan on Tuesday.
His England team-mates Wayne Rooney, Danny Welbeck and Phil Jones all trained with the rest of the squad.
"I am always a trainer who sees the individuals and what each player needs," Van Gaal said.
"Luke needs to be fit and he’s not very fit and can’t perform how I want. He needs to be fit and to train individually.
"I can’t judge why. I see what I see. I have spoken with him and we have made a programme with him.
"He has agreed. We will have to see how long it takes. I don’t know. I have heard good messages from Tony Strudwick the fitness coach."
Van Gaal also confirmed he will give Wilfried Zaha the chance to impress as a striker against Inter, where he will be the last member of United's squad to get a run-out.
The Dutchman has told the England Under-21 international he will have to focus on playing more centrally as he does not fit in elsewhere in his proposed 3-5-2 formation.
Van Gaal added: "He will have to play as a striker as he can’t play the other positions in the system.
"Ashley Young can play as a wing-back. Zaha cannot do that so he will be a striker.
"I have spoken with him and I think he can do it. We will see. He will play the second 45 minutes of this game and will play as a striker."