Speaking in Melbourne on Thursday, Sampaoli said that was mostly down to the depth in his attack, but he could welcome Aguero back.
"We really value him as a player and what he's done at his clubs, especially City," he said.
"We're going to have a chat with him and see how we can move forward depending on where he's at as well.
"It is very difficult when you have three or four really good players to pick only two, so it's really going to depend on how they're feeling."
Aguero is an 82-time international with 33 goals for Argentina, but he has failed to net in any of the eight World Cup qualifiers he has played ahead of Russia 2018.
His last international goal came in June last year – the only one he netted in 2016.