The Blues' boss had to balance the Stamford Bridge books over the summer, selling Demba Ba, David Luiz and Romelu Lukaku to fund moves for Diego Costa, Cesc Fabregas and Filipe Luis.
Despite having the financial windfalls of Champions League football, Mourinho was unable to spend as freely as other sides - with Manchester United a prime example as Louis van Gaal went out and paid high sums despite their lack of European football this season.
United broke the Premier League transfer record to sign Angel Di Maria, with Daley Blind, Marcos Rojo and Radamel Falcao also brought in.
And Mourinho, whose Chelsea side sit top of the table having gone unbeaten in all competitions so far this term, feels more 'traditional' clubs are the beneficiaries of UEFA's imposed financial constraints.
"I think Financial Fair Play is a contradiction," he told Eurosport-Yahoo.
"When football decided to go for Financial Fair Play it was exactly to put teams in equal conditions to compete.
"But what happened really with the 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 joined that elite in the last decade since Roman Abramovich brought the club and began to bankroll improvements on and off the pitch.
Reigning Premier League champions Manchester City fell foul of UEFA's rules as they themselves aim to establish a strong presence across the globe and had their Champions League squad reduced as a result.
And Mourinho believes the rules simply make it more difficult for any club looking to reach the higher echelons of the football world.
"The 'new' clubs - I call them 'new' clubs, those with new investment - they cannot put themselves quickly at the same level," he added.
"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
It's a club with the same owner for more than 10 years.
"A club with a very important history, with great stability too
And 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."
Source : PA
Source: PA