In 2008, McGregor took aim at the veteran actor for supporting a proposed split between Scotland and the U.K., pointing out that Connery has actually lived in the Bahamas for the last three decades.
McGregor later apologised for his remarks, insisting he too shouldn't "dare" to hand out advice to his former countrymen as he also no longer resides in Scotland.
But the Moulin Rouge! star has risked controversy again by revisiting his comments, and branding his fellow Scots "anti-English."
He tells Britain's Live magazine, "I once got involved in (the independence debate) by accident by being flippant at a press conference in Cannes, which was just a stupid thing, and I won't drum it up again. But overnight I found myself on the front of the newspapers as the anti-independent Scotland guy, and I'm neither.
"I've not lived in Scotland since I was 17 years old and I wouldn't dare to say to people in Scotland how they should feel about it, and neither should Connery, in my view. He's lived abroad far longer than I have.
"I like the idea of Great Britain. Scottish-English relations aren't good north of the border. There's a kind of anti-Englishness - or there was when I left - that I didn't like, and I can't imagine that independence would make that any better. There, I've got involved in it by saying I'm not involved in it."