Paine told his opposing captain earlier this month "if you don’t want to come, don’t come” due to some members of the England side unsure if they wanted to travel down under due to quarantine restrictions.
“The Ashes are going ahead. The first Test is on December 8 - whether Joe is here or not,” he added.
“I do know I've got 1,534 more runs than the Barmy Army, so I'm happy with that,” the skipper snapped.
Now Prior has weighed in on the situation, stating Paine's comments go against his 'character', but understands how intense the run-up to an Ashes series can be.
He also said “I've played against him a few times and he's a nice guy, so it's quite surprising to see what he's been saying because it goes against him as a character. He's got a target on his back now.
“The Barmy Army have already pointed out that Joe Root has almost scored more runs this year than Tim has in his entire career, and those are the things that nobody would have even looked at if Tim Paine doesn't say the things that he does."
He added: “The Ashes are unique and everyone gets a bit carried away and it can all get a bit ridiculous, it always has and we know how it works. “For one captain to show a fair bit of disdain and disrespect to another captain is not what anyone wants to see.”
Michael Vaughan, who led England to an historic Ashes triumph in 2005, also criticised Paine for his harsh words.
“As a Test match captain, you have to show a bit of empathy. In the last two years, he [Paine] hasn't taken his team overseas,” he told ABC Sports. “He hasn't had to go through what these England players have gone through. He hasn't gone through what Joe Root has gone through.
“He plays only one format of the game. I do believe he showed a bit of lack of class. I don't think that went down well with the players.
“There is a huge amount of respect between the two sides. And particularly, anyone that's captain of an international side, I personally think he didn't need to say what he said.”
England are looking to regain the Ashes after losing the urn the last time they played in Australia and drawing the return series two years ago.