The Bundesliga side were hit hard by injuries in the first half of the season, losing Subotic as well as other key figures such as Ilkay Gundogan, Marcel Schmelzer and Mats Hummels.
However, Klopp has been boosted by the return to training of Gundogan and Schmelzer, who suffered back and heel injuries respectively, while he is also upbeat regarding Subotic's recovery.
"It's almost like you only need to take the splint away from him, and Neven is able to kick the ball again. Unfortunately, that's not the case yet," Klopp told Dortmund's official website.
"Neven is making good progress. He has another crucial examination on Thursday, and then we will know more about his recovery.
"We want (Hummels) to use the next two weeks to catch up on his fitness."
Klopp also stated his confidence that striker Robert Lewandowski, who agreed a deal on Saturday to join Bayern Munich when his contract expires at the end of the season, will focus on his current employers for the remainder of the campaign.
"It was (the) best time to do what had to be done, during the winter break," he added.
"We had known for some time that Robert would leave us. His full focus will now again be on Borussia."
While Jurgen Klopp's men were able to qualify for the knockout stage of the Champions League, they won just one of their six league matches prior to the mid-campaign break and slipped to fourth in the table.