Chelsea have hit out at FIFA's "deeply unsatisfactory" conduct when imposing a two-window transfer ban on the west London club.
The Court of Arbitration for Sport (CAS) has lifted FIFA's transfer embargo on Chelsea following the Premier League club's appeal against the sanction relating to the signing of overseas youth players.
The Swiss-based CAS halved FIFA's transfer ban to one window, leaving Chelsea free to seek new recruits in January.
Chelsea have reacted to the CAS findings by branding elements of FIFA's approach "perverse", warning that the global governing body risks undermining itself through "inconsistent and unequal sanctions".
Manchester City avoided a FIFA transfer ban in August despite being found guilty of breaching rules on youth signings, and now Chelsea have questioned the governing body's conduct.
"The approach taken by FIFA to this case has been deeply unsatisfactory, not least as FIFA chose to treat Chelsea entirely differently to Manchester City for reasons that make absolutely no sense to Chelsea," read a Chelsea statement.
"Chelsea respects the importance of the work undertaken by FIFA in relation to the protection of minors and has fully cooperated with FIFA throughout its investigation.
"However, if FIFA continues to impose inconsistent and unequal sanctions on clubs then it will not only undermine the very purpose of the regulations, but it will also bring into doubt the game's confidence in FIFA being able to appropriately regulate this important area."
Chelsea's continued frustrations at their original punishment led the club to mine into the detail of FIFA's findings, once CAS had upheld the Stamford Bridge outfit's appeal.
"FIFA accused Chelsea of having breached Article 19 of the FIFA regulations in relation to 27 players, covering the period from 2009 onwards," read the Chelsea statement.
"Of those, 16 players were registered by Chelsea in exactly the same way as other Premier League clubs registered players at the time.
"Furthermore, Chelsea sought clarification from the Premier League in 2009 about whether it needed to apply for permission to register players in this category.
"The FA subsequently liaised with FIFA and it was confirmed to Chelsea that players in this category were entitled to register and that no special application was required (and in fact no special application process existed).
"Accordingly, the fact that FIFA brought charges against Chelsea for this category of player was perverse. We are grateful that this appears to have been corrected by the CAS."
Chelsea insist another group of players whose registrations FIFA questioned were only regulation breaches of a "procedural nature". And the Premier League club further criticised FIFA over the governing body's own definition of a player registration.
"With respect to the remaining five players, FIFA's position was that it "deemed" these players to have registered prior to any application for registration being made," read the statement.
"Chelsea maintains, as was held by CAS in the Real Madrid case, that the FIFA regulations do not cover a concept of "deemed registrations" and accordingly it is not open to FIFA to "deem" that registrations were made before they were in fact made."
The PA news agency has contacted FIFA for a comment.
Chelsea boss Frank Lampard welcomed the ability to make signings in January but conceded the Blues must go about their recruitment carefully.
Asked about the transfer market, Lampard said: "It will be a challenge, yes. Personally what affected me in the summer with the transfer ban, when you come into the club or when you want to go a certain way, sometimes the players you bring in and the attributes they have are key to that.
"I couldn't make those changes to bring in the players that I felt would help the way I wanted us to play.
"As much as it is important to bring players in, it is as important for me that we keep the balance of the squad right.
"It will be a challenge and hopefully we will get it right."
