Martinez was left out of the squad for Sunday’s 3-0 defeat to Crystal Palace after Emery deemed the Argentina international was not “100 per cent focused”.
United are choosing whether to pursue a move for either Martinez or Royal Antwerp goalkeeper Senne Lammens and are not yet believed to have made a formal bid.
But the distraction of fresh speculation was enough for Emery to make his decision.
Asked about Martinez’s omission, he replied: “He was not available. Tomorrow is the deadline and we will see how we are finishing.
“We need the players focused and 100 per cent and he wasn’t.”
When they asked if Martinez could still remain at Villa beyond the deadline, Emery said: “We will see tomorrow. Sorry, I can’t tell you anything more. The reality is I don’t know.
“We are working with everything we have now around us. But I am confident we are going to start again after the break with a new energy, with focus completely and no doubt.”
Martinez’s future has been the subject of speculation since he left the pitch in tears following the final home match of last season.
United and Atletico Madrid were both interested but did not firm up their interest and the World Cup winner looked destined to stay until United’s poor start to the new campaign.
Any move now will be dependent on the Red Devils matching Villa’s valuation and the latter sourcing a replacement.
Villa’s summer has been one of frustration, with the club’s spending restricted by Uefa’s financial regulations.
Several players, meanwhile, have been linked with moves away and Emery, whose team are yet to score a goal after three matches, suggested the ongoing speculation had contributed to their poor start.
He said: “It is not helping us. This is one of the circumstances we have which is not helping.
“But tomorrow we will see how we close the window.
“We have a lot of circumstances which are not helping us to be mentally like we were last year.
“But after tomorrow we are going to set everything.
“When you are getting the level we achieved and you are in a moment like we are now, one point from three matches, you are more frustrated than normal.
“To keep balance now is my message. I am confident how after tomorrow how we will manage the group we have.”