"The dynamics definitely changed. It became more groups in the team. It wasn't a team as so. There was different little factions going on and it was very toxic," Johnson told Fox Sports News.
"It just built very slowly but everyone could see it, everyone could feel it and nothing was being done at that time.
"So it wasn't a very enjoyable place to be and you're supposed to be enjoying yourself when you're playing for your country.
"It was a pretty bad experience, bad time, a couple of us didn't want to play.
"Even some of the young guys coming through could see it a mile away and they didn't enjoy it, they said state cricket's so much more fun."
Johnson noted he wasn't on the best terms with Clarke following the homeworkgate suspension.
"I didn't take it too well," he said.
"I guess the relationship was pretty strained at that point of time within the team ... I definitely felt like an outsider."
Clarke has been a near-constant presence in the headlines over the past fortnight following the release of his biography, which raises concerns about the current power dynamic in Australian cricket and revisits his run-ins with Shane Watson and Simon Katich.