Bashir said he refuted any allegations of "distortion and misrepresentation" levelled at him and the programme.
The journalist was answering questions on a live ITV.com webchat about the making of Living With Michael Jackson, which was broadcast on ITV1 last week.
Bashir said "it wasn't a traumatic experience" for Jackson but that "press coverage has been difficult for him".
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I did not set out to ensnare him with a child
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Martin Bashir
"If concerns are expressed about the way he behaves with children and it makes him careful in the future then that's a good thing," he added.
Jackson has been widely criticised since revealing on the programme that a 12-year-old called Gavin regularly stayed at his mansion and slept in his bedroom.
During the webchat, Bashir discussed how Gavin was introduced to him during filming.
He said the boy's relationship with Jackson caused him "deep concern".
Bashir said Jackson was "brilliant with his own children" but added that there was "concern about the way he relates to children who are not his own".
"I did not set out to ensnare him with a child," he added.
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The film was fair to his musical achievement and gave him every opportunity to explain himself
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Martin Bashir
"I was curious about the relationship and they volunteered this aspect of their relationship.
"I became disturbed by that and I don't think that's unreasonable."
Bashir said he "was not accusing anybody of being a child molester or a paedophile".
The webchat followed the release yesterday of a video clip showing Bashir praising Jackson's parenting skills.
The footage shows Bashir telling Jackson that his relationship with his children "almost makes me weep" because it is "so natural, so loving, so caring".
The clip comes from a two-hour special, tentatively called Michael Jackson, Take Two: The Interview They Wouldn't Show You, being screened by Fox TV in the US next Thursday.
Bashir said a 16-second clip was being used to portray him as being unfair when he had interviewed Jackson for more than 10 hours.
"The film was fair to his musical achievement and gave him every opportunity to explain himself," he said.