Jota was forced off the pitch after 30 minutes of Sunday's 2-1 Premier League victory over Chelsea with right back Conor Bradley missing the game entirely due to injury.
Liverpool were already without goalkeeper Alisson Becker, forward Federico Chiesa and midfielder Harvey Elliott through injury, none of whom have travelled to Germany for Wednesday's match.
"Conor Bradley, Harvey Elliott, Federico Chiesa, and Alisson didn't make the trip so we have a few issues at the moment," Slot told reporters.
"Diogo got a knock when he was trying to go to goal, he was brought down but the other player fell on to him, and that hurt him and he couldn't continue to play and come with us.
"It is difficult to judge at this moment of time to see how long it's going to take."
Liverpool have won both their fixtures in Europe this season, while Wednesday's opponents have lost their opening two encounters in the new-look competition that features a 36-team league rather than four-team groups.
Slot, however, said it was too early to judge how teams were doing as the "league table doesn't tell the whole story."
"The concept of the Champions League (as far as) I got my head around it - I don't think you can have a fair opinion yet because we are only two games into the Champions League now," Slot said.
"We've to wait and see what the result of this format is and you can only judge that after the group stages are done."
