City - and Chelsea's Champions League last-16 opponents Paris St Germain - were issued heavy fines by UEFA for their outlandish spending in recent years
Regulations dictate clubs should spend within their means.
Chelsea, who are five points clear of City after their 1-1 draw last weekend, are bidding to comply with FFP and made a profit for the third successive transfer window despite signing Colombian World Cup ace Juan Cuadrado on Monday's deadline day.
"I enjoy the challenge of the English competition," said Mourinho, speaking ahead of Saturday's trip to Aston Villa.
"It's a good challenge
The only thing that is not nice is that you compete against the ones (clubs) who don't follow the same rules.
"That's the only problem
I don't think - and it's happened before - a team can be champions when you are punished because you didn't comply with Financial Fair Play."
City were fined £49 million last May, after winning the 2013-14 title, for infringing FFP regulations, but made the biggest English outlay of the transfer window in spending £28m on striker Wilfried Bony.
Asked what the penalty should be, Mourinho said: "Points
Of course
I don't know (how many)."
It is not the first time Mourinho has spoken of City's spending.
Mourinho, who spent lavishly during his first spell as Chelsea boss from June 2004 to September 2007, is happy with the transfer strategy imposed at Stamford Bridge by owner Roman Abramovich.
Chelsea sold Andre Schurrle to Wolfsburg for a reported £8m profit on a player bought 18 months previously from Bayer Leverkusen, allowing them to buy Cuadrado from Fiorentina.
The sale of Ryan Bertrand to Southampton for a reported fee of £10m allowed the Blues to make a profit once again as Mourinho reshapes his squad.
Mourinho, who is 18 months into a four-year contract, added: "It was explained the profile of club Mr Abramovich wants, with total, complete respect to the Financial Fair Play rules.
"Our work to keep the team strong, with possibility to compete against the ones financially more powerful or against the ones who don't care and don't respect Financial Fair Play..
we had to work very, very hard.
"In my area, I tried to do that
Analysing the players we can sell and those we can buy.
"But when it goes to numbers, it goes completely out of my control
Total credit to the people who deserve credit in that area."
Mourinho refused to speak about Manchester City, but did sarcastically rebuke Manuel Pellegrini for saying Diego Costa "needed to change" after the Chelsea striker was banned for three matches for stamping on Liverpool's Emre Can.
"I don't speak about Man City their players and their options," Mourinho added.
"I appreciate the lesson that Mr Pellegrini wanted to give to one of my players, but I don't want to do the same or give any kind of word about it."
Despite defeat to Tottenham and draws with Southampton and City, Chelsea have increased their lead in recent weeks.
Mourinho, who was fined £25,000 for saying there was a "clear campaign" against his side and was on Friday speaking for the first time in 10 days after a self-imposed media blackout, thinks his side should have had more points.
"We had lots of unlucky situations," he said.
"Crucial moments in crucial matches cost (us) points."
Asked how many points, he said: "Get the fixtures
See the points
See what happened
You don't need to be an expert in maths to do two plus three, three plus one, and you will arrive at your conclusion easily."
Source : PA
Source: PA