Scott Hogan is absent from the Brentford squad for their game at Wigan, despite travelling with the squad to the DW Stadium.
The striker has been heavily linked with a move to West Ham during the January transfer window and has not featured for the Bees since the 2-1 win at Birmingham.
He was rested with a glute injury against Eastleigh in the FA Cup but was an unused substitute for Brentford in their 2-1 defeat to Newcastle.
Hogan's presence on the bench caused consternation and Smith was pressed on the situation after the game with the Magpies.
"I made a decision on Thursday not to start Scott, I made Scott aware of that and Scott was happy with that. I felt that Romaine Sawyers and Lasse Vibe deserved to keep their place in the team," Smith said after the game with Newcastle.
"There has been a lot of speculation and offers for Scott, so it has been very difficult for him.
"Scott was available for selection, I decided not to select him for the long-term interest of the football club because the two players last week have done really well.
"If I was to leave one of them out and put Scott in and he was to go on Monday it wouldn't help - the long-term interest of the football club has always got to be at the front of my mind."
Despite that, supporters felt that Hogan refused to play; something Smith categorically denied.
He said ahead of the game: “It's unchanged from last week. Scott is still available for selection. He was last week. I chose not to play him and then chose not to bring him on.
“He's trained all week and that will be my decision if he plays or not.”
He added: “Scotty has been brilliant since I've been here. We spoke on Friday.
“I made my decision on the Thursday regarding the team and him being on the bench and he knew my reasons for it and was happy with that. He now comes into contention to start.”
Brentford team to face Wigan: Bentley, Egan, Dean, Bjelland, Colin, McEachran, Yennaris, Woods, Field, Sawyers, Vibe.
Brentford substitutes: Bonham, Hofmann, Kerschbaumer, Clarke, Jota, Barbet, Cole.