Mourinho's club spent heavily in the close season to sign Cesc Fabregas and Diego Costa but, after losing a number of players, had a substantially smaller net spend than rivals such as Manchester United and Barcelona.
The regulations were designed to limit reckless spending and make clubs operate within their means but the Portuguese said the rules have failed in their primary objective to create equal conditions for all.
"I think Financial Fair Play is a contradiction because when football decided to go for Financial Fair Play it was exactly to put teams in equal conditions to compete," Mourinho said in an interview with Yahoo.
"But what happened really with Financial Fair Play is a big protection to the historical, old, big clubs which have a financial structure, a commercial structure, everything in place based on historical success for years and years and years."
Chelsea have been among the Premier League's heaviest spenders since Russian billionaire Roman Abramovich took over as owner in 2003.
Mourinho, however, said the regulations were subduing clubs with new investment to help maintain what he perceives is the hierarchy of Europe's biggest teams.
"The 'new' clubs, I call them 'new' clubs, those with new investment, they cannot put themselves quickly at the same level," he explained.
Manchester City and Paris St Germain, clubs with recent investment, were hit in May with heavy fines for failing to comply with the regulations.
"Clubs with new owners cannot immediately attack the control and the domination of these big clubs. Chelsea is not an old, historical, huge club but it's also not a club with a new owner," added Mourinho who is Yahoo's global football ambassador.
"It's a club with the same owner for more than 10 years. A club with a very important history, with great stability too.
"At this moment I think we are just below them. I can say we are a very good club with the ambition to be a great club."
In October, president Michel Platini said European football's governing body UEFA had held "constructive" and "encouraging" discussions about FFP with the top clubs.
(Editing by Tony Jimenez)
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