National Leader Simon Bridges said the situation "did seem wrong".
"You have a situation where there were clear conflicts; where some people may think they can get access to the Prime Minister through him and he hasn't declared, and he hasn't been clear on that."
He said there was a perception of a conflict of interest and called on Ardern to "clear it up".
Act Leader David Seymour also said it appeared as if the conflict was not managed properly.
Speaking to media, Ardern said she was comfortable with how Ministerial Services managed the issue.
"He [Thompson] managed directly his conflict of interest with ministerial services – that was something he dealt directly with them on, not through me as that would not have been appropriate."
She said she did not discuss Thompson's clients as that would have not been appropriate.
Thompson took over as acting chief of staff as the previous man in the job, Mike Munro, was ill.
"It's not easy to find someone who has a level of knowledge and experience and GJ Thompson had worked in this building before and was able to take a short leave of absence to cover for the period we needed."
In a statement, Thompson said any potential conflicts of interests were declared and managed at the time
"I took a leave of absence from the firm. The arrangements made reflected the short-term nature of the role."
He told The Herald the idea that he hadn't done everything by the book was "erroneous".
Asked if he had declared his clients to Ministerial Services, Thompson did not directly answer the question, only saying: "I did what was required by Ministerial Services to manage the conflict."
The Department of Internal Affairs, the branch of Government in charge of Ministerial Services, said it would treat any questions about the potential conflict of interest as an official information act request.