Her outspoken comments included criticism of a freshwater scientist, dismissal of scientific concerns about a prominent weed-killer, and describing irrigation as a "great boon" to the environment - which outraged environmentalists.
The then-Prime Minister's chief science adviser Sir Peter Gluckman said many of Rowarth's comments were inappropriate for a regulator, and passed his concerns to the authority.
Environment Ministry chief executive Vicky Robertson also expressed concerns to the authority.
When Freeth fronted the select committee, he had angry exchanges with National's environment spokesman Scott Simpson, who asked Freeth if he could expect "straight unequivocal answers".
Simpson said Freeth had previously been recalled to the committee to correct previous information, but Freeth rejected this.
"I want to be assured that we will get straight answers to straight questions," Simpson said.
Freeth was initially reluctant to talk about the terms and conditions of Rowarth's departure.
"Employment matters are confidential, and the nature of the agreement with Jacqueline was such that we would respect that," he said.
Simpson said the authority was a state-funded entity.
"I don't think questions relating to the extraordinarily odd circumstances surrounding the early exit of the former chief scientist and the financial payouts that were part of that ... is outside the purview of the committee."
Freeth eventually conceded the $143,853 figure paid to exiting staffers included a payout to Rowarth.
When Simpson asked if Rowarth had been contracted to work after she had left, Freeth said: "No, and I'm getting a little tired of this. I find it somewhat offensive."
Simpson: "That's an unequivocal no? ... I'm naturally dubious and I think I have good cause to be."
Freeth: "I reject what has been said in terms of last year's experience. I'm perfectly happy for this to be tested outside of Parliament."
Simpson later asked if scientific independence was "only available when it suits the collective narrative", to which Freeth replied: "I object to the questions asked, and the answer is no."