Ferrero made the comment in an interview with RAI, discussing Massimo Moratti's decision to resign as Inter's honorary president.
"Moratti is a great man and it seems unfair that he has been treated like this, because he has given so much to Italian football," Ferrero said.
"I am very sad for him. I had told him: 'Kick out that Filipino...'"
In a statement on the club's website, Ferrero apologised and said his intention was to praise Moratti.
"I didn't want to disrespect Mr Thohir, the directors of Inter or the people of the Philippines with whom I have a wonderful rapport," he said.
"I wanted to praise Massimo Moratti and all that he has given to Inter and to Italian football over the last 20 years."
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