This morning Jones was defiant about not needing to remove himself from the meeting, but Ardern said he had softened his stance when discussing it with her this afternoon.
"He agrees in hindsight it would have been helpful for him not to be in the room," Ardern told media at her post-Cabinet press conference today.
"Minister Jones himself would acknowledge that would have helped a perception issue. But he has been given guidance on managing the conflict after he declared it, and he has followed all of that advice."
Jones had delegated the decision-making about Manea to other ministers and did not receive official briefings on the project, she said.
Act and National have criticised Jones' role at the meeting as well as his answer to a written parliamentary question, which said that he had had "no formal meetings regarding the Manea Footprints of Kupe project since receiving my ministerial warrants".
Act leader David Seymour has written to Auditor-General asking him to investigate Jones' involvement, which he called "completely inappropriate" and grounds for him to be sacked.
Questions are also being asked about how Jones raised the conflict of interest.
Responding to a written parliamentary question in May last year, Jones said he raised it with the Cabinet Office in late November 2017.
But the Cabinet Office's latest release of declared ministerial conflicts of interest from when the Government took power in October 2017 to September 2018 does not include Jones.
A spokesman for the Prime Minister said that Jones raised the conflict of interest verbally, and that the Cabinet Office's list was not exhaustive.
Jones has downplayed his link with Manea, saying he met with the late Whetu Naera, a Hokianga chief and key proponent of the project, when he was a Labour MP in 2014.
That led to Manea applying for Government funding and sending documents to MBIE in 2014. The documents proposed Jones as chairman of the project.
"Someone, I'm not entirely sure, communicated to the Government in 2014 or 2015 that I was going to be the chair of a trust to drive this project forward," Jones told Radio NZ this morning.
"Just because I turn up to a meeting and make a positive impact on people - after all, everyone wants Sonny Bill in their team - that doesn't mean I was the chairman or director. It means I was at a random meeting five years ago."
Jones said this morning he did not need to remove himself from the ministerial meeting in February, which included Robertson, Tourism Minister Kelvin Davis, Economic Development Minister David Parker and Transport Minister Phil Twyford.
"Just because you declare a perceived conflict of interest doesn't mean you are tongueless or voiceless.
"It is not necessary for me physically to leave every meeting. I may find myself in very few meetings."
National Party regional development spokesman Paul Goldsmith said Jones needed to explain his actions.
"The Prime Minister should haul him into the office and get him to reconcile what appear to be irreconcilable statements: that he wasn't involved, and that he was at the meeting and seems to have been very active."
