Ferrero was discussing former Inter owner Massimo Moratti's decision to resign as the club's honorary president this week amid media speculation of a disagreement with Thohir.
"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 during a live programme on Italian state broadcaster RAI.
"I am very sad for him. I had told him: kick out that Filipino..."
When the programme presenter told him that Thohir was Indonesian, Ferrero replied: "Don't defend him, he's insulted an emblem of Italian football."
Shortly afterwards, Sampdoria issued what they described as a sincere statement by Ferrero on their website.
"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."
Ferrero's outburst came less than three months after Carlo Tavecchio, now president of the Italian football federation (FIGC), referred to African players as "banana eaters".
Tavecchio caused an outcry when he made a comment about a fictitious African player he named Opti Poba "eating bananas" during the campaign in which he beat former Italy and AC Milan midfielder Demetrio Albertini for the FIGC presidency.
A FIGC investigation found there was no case against Tavecchio, however a separate investigation by European football's governing body UEFA barred him from holding any position within UEFA for sixth months or from taking part in next year's UEFA Congress.
Inter won five Serie A titles during Moratti's 18-year reign, in successive years between 2006 and 2010, and also clinched the Champions League and UEFA Cup once each and Coppa Italia four times.
Last year, Moratti sold a 70 percent stake in the club to a consortium led by Indonesian business tycoon Thohir, who replaced Moratti as club president.
(Writing by Brian Homewood in Berne, editing by Mark Meadows)
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