Joyce said today that the apology was part of a legal settlement which also included Hooton paying for his fees. He would not disclose the amount paid to him.
Joyce began defamation proceedings after Hooton wrote a column in the National Business Review on March 2, titled "Joyce sacking first test of Bridges' leadership".
"This article could reasonably be understood to suggest that the Hon Steven Joyce had engaged in unethical, dishonest and/or corrupt behaviour during his tenure as a Minister in the previous National Government," Hooton said in a statement today.
"Nothing in the column was intended to convey such suggestions, which would be untrue. I apologise to Mr Joyce for any harm caused as a consequence."
Joyce, a former Finance Minister who resigned from Parliament last month, said politicians should expect robust criticism but he drew the line at defamatory comments.
"The particular article that Mr Hooton wrote I believed was defamatory, took a legal case and he's decided to settle it, and that's the apology that is being made today."
It has previously been reported that Joyce was upset at Hooton's allegation that the MP only received four caucus votes in National's leadership contest, but Joyce said that was not correct.
"That wasn't one of the particular issues," he said.
Joyce has also taken a defamation case against the NBR, which is refusing to back down.
The newspaper ended its relationship with Hooton soon after the column was published. But the article remains on its website.
Publisher Todd Scott said on Twitter that Hooton had "cut a deal" without consultation with his company.
Hooton, the managing director of PR firm Exceltium, is now a columnist for the New Zealand Herald.
