Ecclestone suggested that insults thrown at Hamilton via websites in the build-up to the Brazilian Grand Prix, as well as earlier this year during testing, were not racially motivated.
"There were a few people in Spain and that was probably beginning as a joke rather than anything abusive," Ecclestone told BBC Radio Five Live.
"I think people look and read into things that are not there. All those things are all a bit of a joke and people are entitled to support who they want. I don't see why people should have been insulted by it."
Those comments have caused a big controversy in Britain - with some leading anti-racism campaigners believing Ecclestone's statements were unacceptable.
Kick It Out, the anti-racism sports pressure group, told The Times: "What Bernie Ecclestone said is shocking and disgraceful. In his position in Formula One, and with the sway that he holds, for him to come out and say this . . . is very worrying and short-sighted.
"You would expect [him] to be protective of someone like Hamilton and use his authority to chastise these supporters. This will upset a lot of people, particularly young mixed-race and black males who are looking up to Hamilton and what he has achieved.
"Fans blacking up in the stands was overt, old-school racism and that is still fresh in the memory. People are entitled to support who they want but that is no reason for racist abuse, which this clearly was."
Former footballer Paul Elliot, who is ambassador for European campaigners Football Against Racism in Europe, was widely quoted in the British press as saying: "The comments are shameful and disgraceful. Lewis Hamilton has made a colossal contribution to the country and the sport, and the sport has a duty of care to protect him and his family.
"Bernie Ecclestone is not fit to be in that environment and he should resign. There has to be zero tolerance. However successful Ecclestone is, it is clear he is out of touch with the 21st century. It is totally out of order, unacceptable and he should move over."
Hamilton also said that there was little humour to be found in the actions of fans who dressed up in black face paint and black wigs - although he had not heard exactly what Ecclestone had said.
"I didn't see it as a joke," he told a press conference for Vodafone. "It's something that happened but it is in the past.
"What's more important to me is that I had a lot of support, especially from UK fans. As long as I have my country behind me it makes me very proud. It makes me very proud to see my fellow countrymen holding up the flag. All the other stuff I need to put behind me. I don't generally keep up with what's being said and I haven't read what Bernie said."
Ecclestone reacted to the controversy his comments had caused by denying he was condoning racist behaviour.
"I was the one who pulled the Grand Prix out of South Africa [after 1985] in support of Nelson Mandela because of bloody apartheid before these people knew anything about racism," he told The Times.
"I said to the promoters in Barcelona, 'Let me go and get the people that blacked their faces up and bring them into the paddock and introduce them to Lewis and then see what they've got to say.' But the police said, 'Don't do it.' I personally was going to get them."
