World football's governing body had asked both clubs for information about Pogba's world record $156 million transfer from Juventus, following leaks which claimed to give details about the huge deal.
A book titled, "The Football Leaks: The Dirty Business of Football" alleged Pogba's agent Mino Raiola had made over $62 million from the deal, $42 million of which was paid by Juventus.
"We can confirm that disciplinary proceedings have been opened against Juventus FC. As proceedings are ongoing please understand we cannot comment further at this stage," FIFA said in a statement.
"We can also confirm that no disciplinary proceedings have been opened against Manchester United".
FIFA did not give details of the nature of their proceedings against Juventus but some media reports have suggested it could be related to breaches of third-party ownership rules.
In April 2015, FIFA announced the banning of third-party ownership, barring either clubs or players from entering into economic rights agreements with third-party investors.
In an interview with the Financial Times last October, Italian-Dutch agent Raiola said: "In this deal Juventus was not the only owner of the player's rights". The report also cited both the agent and Juventus as denying there was third-party ownership relating to Pogba.
Photo: PHOTOSPORT Manchester United midfielder Paul Pogba.