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The Portuguese tactician angered residents of the city by comparing it to Oporto and suggesting that bodyguards were necessary to visit.
However, the Blues chief has penned an open letter of apology to Italian senator Carlo Vizzini, insisting he meant no offence.
"I am very sorry that I have offended you and Palermo's people with the declarations ascribed to me," wrote Mourinho.
"I never had the intention to offend, and I want to publicly apologise to you and Palermo.
"I have enormous respect for Sicilians and for all Italians in general.
"I was trying to underline the behaviour of others, not of your fellow citizens.
"What happened is an unpleasant incident and I hope you will accept my apologies."