On Wednesday, FIFA hit the Liga champions with an embargo for the next two transfer windows due to irregularities with their dealings over youth transfers, although the club have since announced their intention to appeal the decision.
Ter Stegen's agent Gerd von Bruch initially moved to allay fears that Barca's ban could hinder any agreement being reached between the two clubs amid intense speculation that the 21-year-old is on his way to Spain.
But a spokesperson for world football's governing body has cast doubt on the prospective deal.
A statement released to Perform read: "In principle, the transfer ban prevents the club from registering any player for the next two complete and consecutive transfer periods (summer 2014 and winter 2015 registration periods)."
Von Bruch has since moved on his original position, conceding the transfer would be "impossible" judging by FIFA's declaration.
Speaking to Sport Bild, he said: "At this stage - if I interpreted the FIFA statement right - Marc-Andre ter Stegen's move to Barcelona in summer is impossible."
Barcelona are on the hunt for a new goalkeeper with long-term number one Victor Valdes previously announcing his decision to depart Camp Nou at the end of the season.
It has been widely expected that Ter Stegen will fill the void, after the Bundesliga side confirmed the youngster will leave the club when the current campaign ends.
The ban could also cause problems for Barcelona in defence, with captain Carles Puyol having previously revealed his decision to end his long association with the club.
Barca's appeal may be boosted by the fact that Chelsea had a similar sanction overturned by the Court of Arbitration for Sport in 2010 after being hit with an 18-month embargo over the transfer of French midfielder Gael Kakuta.
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