Other than former Manchester City captain, Gundogan, who joined on a free transfer in June, new signings Inigo Martinez and Oriol Romeu have also not been registered.
Players such as Ronald Araujo, Marcos Alonso, Sergi Roberto and Inaki Pena, who signed new contracts, also remain unregistered.
That means the Spanish champions have only 12 players available for their season debut.
Barça experienced the same situation last season, when they were blocked by La Liga's strict financial regulations to register new signings such as Robert Lewandowski, Franck Kessie, Andreas Christensen and Raphinha.
They were eventually registered on the eve of Barça's season opener after the club triggered a last-minute economic operation.
Defender Jules Kounde, however, ended up missing several games as his formalities were not completed until the end of August.
Clubs have to meet La Liga's salary cap to register new signings as well as those who sign contract renewals.
Last year Barcelona resorted to selling club assets as "economic levers" to create the margin they needed with La Liga, as their debts totalled 1.35 billion euros.
They will not be able to play at Camp Nou for the next few seasons after agreeing a financing deal worth 1.45 billion euros to renovate the iconic, but outdated stadium.
The 100,000-seater venue was the club's biggest source of income and they will have to be creative to stay competitive within the restrictions of La Liga's FFP rules for the second season in a row.
Last year the club signed a shirt and stadium sponsorship deal with audio streaming platform Spotify in an agreement worth 280 million euros.
They also agreed to sell a 25% stake in their 'La Liga TV' rights for the next 25 years to U.S. private equity group Sixth Street (TSLX.N) for 607.5 million euros and approved the sale of a minority share of their audio-visual division to Socios.com and Orpheus Media for 200 million.
It has been reported that they are trying to sell another percentage of their audio-visual division to generate the margin they need to meet LaLiga's salary cap numbers.
