"It signals we need to improve the way we engage with athletes and better understand what their needs and concerns are," said Scott.
"We've also invited the New Zealand Olympic Committee's athletes' commission to be part of that process - so the relationship's not exclusive - but we recognise each of them as a key stakeholder in improving our dialogue and relationships with high performance athletes."
"As a result, New Zealand can develop a competitive edge on the global stage which is sustainable across generations."
NZAF chairman Rob Nichol said HPSNZ has an impact on plenty of their members.
"We want to have a strong relationship and dialogue [with them] and we've been impressed and refreshed with the leadership that's come into high performance sport at the moment.
"[This agreement] gives us an ability to pick up the phone to table issues.
"The earlier you look at these things the better within these environments. Having that relationship will be crucial."
A debate over whether the Athletes' Federation should receive annual Government funding is also expected in the coming months.
Scott says any funding of the NZAF or similar players' associations will likely come as part of a 2030 blueprint being worked on over the next 12-14 months.
"One of the questions being asked is: Do we need an independent athletes' voice with which organisations such as HPSNZ can liaise and consult? Those things are a possibility as part of this."
The 2030 Blueprint project is led by business consultant Paula Halliday.
"We're looking at key facets of the high performance system, what that should look like by 2030 and how we futureproof it," said Scott.
"That involves athlete well-being, an investment strategy, coaching, pathways for athlete development, sports science, and medicine and training facilities. How do we build that into a sustainable system?
"We need to engage with the sports sector to get that right. It's not something where you switch a light on and it's done."