Some viewers of the new series reacted badly to a recent prank during which Flintoff cracked a watermelon over Harris' head.
However, the presenter has hit back, saying that he's never felt bullied by the actions of his co-presenters.
The 44-year-old tweeted: "Need to tell you all that Fred and Paddy are two of the kindest people I've worked with. We're good pals and I've never felt remotely picked-on.
"I'm small - so what? We all give as good as we get. And who gets to slide the supercars? Me! It's just telly, and I'm loving it!"
In an interview with Piers Morgan and Susanna Reid on Good Morning Britain, Harris also referred to Flintoff and McGuinness as 'national treasures' and 'brilliant entertainers' before adding: "And I do the geeky stuff in the background, it's a good mix!"
He said: "I love a bit of rough and tumble, I was brought up that way, I went to school that way.
"I wasn't prepared for it [the prank] and I love it - it's what it should be about.
"If you mess around with your mates, you get into rough and tumble then you remember you're in your mid-40s and you can't land the way you used to, so it's great fun."
Speaking about Flintoff - the former Ashes winning England cricketer - Harris called him a 'unit' and said: "He's strong, man, I mean he picked me up and threw me around the way I throw around my nine-year-old."
Paddy's not exactly small either.
Whatever the guys are up to, it appears to be working. After the show lost veteran presenters Jeremy Clarkson, James May and Richard Hammond some years ago, it has looked to be finished at various points.
However, after a period of poor ratings under hosts such as Matt LeBlanc and Chris Evans, the show appears to have struck upon a format that the public like once again.
In fact, it's the highest rated show on BBC Two so far this year.
A representative for Top Gear told The Metro: "Top Gear's producers do not, and never will condone bullying in any shape or form - on or off screen.
"As we hope the series has demonstrated so far - Paddy, Freddie and Chris have become great friends who enjoy teasing each other relentlessly during every challenge the producers set them."
Top Gear continues on BBC Two this Sunday at 8pm.
Featured Image Credit: BBC Two
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