Council environmental officer Peter Wilson said the council was one of the parties in an Environment Court mediation process over 6A in late 2013.
Fish and Game had itself first suggested an "oversight'' group for implementation of the 6A water quality changes should be established, he said.
But about two years later the group, as envisaged in the mediation agreement, had not yet met.
A technical group, largely consisting of rural industry groups, including Federated Farmers, has met quarterly for some time.
"We support 6A ... 6A implementation can't succeed without environmental interest groups being part of the stakeholder committees,'' he said.
Fish and Game Otago had a statutory role to protect Otago's fishing and game habitat, including fresh water.
It would be "disappointing'' if the organisation that had suggested holding oversight meetings was itself not included, Mr Wilson said.
Fish and Game is part of an Otago Regional Council river low-flows stakeholder group, which met on Monday.
Fish and Game had a positive overall relationship with the ORC, which had improved significantly in other areas over the past two years, Mr Wilson said.
But the lack of committee links with the ORC over 6A implementation was "a little bit of a head-scratcher'' and time was starting to run out before 6A was fully implemented in early 2020, he said.
Community submissions to the ORC's latest long-term plan last year repeatedly emphasised the need for closer engagement between council and the community.
Several submitters had queried what had happened to the promised stakeholder group.
ORC director external engagement Caroline Rowe said it was envisaged there would be two stakeholder groups - "one technical, the other high level'' - involved over 6A implementation and the Otago water plan.
Fish and Game Otago was "a key stakeholder'' and she saw it as a likely member of the "higher-level'' group, she said.
Asked about Fish and Game's exclusion from the technical group, Ms Rowe said she was new in her job, and was looking at how some of the ORC's relationships could be improved overall, including when groups were undertaking collaborative work.
The second proposed stakeholder group was a "high-level advisory'' body whose purposes included making "input to any required change to the strategic approach'', and to "nationally communicate the learnings and achievements'' from implementing the water quality provisions.
This group's membership had yet to be confirmed, and representation on it was likely to be "both national and regional'', she said.
It was a "priority'' to establish the group early this year, she said.
