Premier League champions Manchester City, who face Chelsea in a heavyweight clash between the two title favourites on Sunday, were fined 60 million euros (51.11 million pounds) in May for breaking the rules, but the Portuguese believes stricter sanctions should be imposed.
"Are the fines fair? I don't think so. What is fair is to remove points and titles," the 51-year-old was quoted as saying by British media.
"If you win titles and are then penalised economically, you continue."
The FFP rules, which were set up by the Club Financial Control Body (CFCB) in 2012, are designed to limit financial losses and make football clubs more financially stable.
City have spent heavily since their takeover by Abu Dhabi's Sheikh Mansour in 2008 in an attempt to cement their place among Europe's elite sides.
FFP rules also dictated that their squad for this season's Champions League was capped at 21 players rather than the usual 25, but Mourinho suggested the punishment was not enough to dissuade repeat offenders.
"If you have to take one or two players off your list for the Champions League and instead of going with 24 go with 22, no problem," he added.
"But say you start the next championship with six points deducted, which means that you don't play in the Champions League, but in the Europa League, that is more serious."
Since Russian billionaire Roman Abramovich took over Chelsea in 2003 the west London club have been among the Premier League's biggest spenders, but Mourinho insisted they will adhere to the rules.
"The teams that benefit from this are the most powerful economically, with more history and more followers. Right now, with FFP, we have become a team like any other, managing our resources in a rational manner."
(Reporting By Tom Hayward; editing by Toby Davis)
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