Federated Farmers president Bruce Wills said the organisation's farm confidence survey showed those concerns appeared related to regional council water quality proposals.
Many respondents cited Horizon Regional Council's One Plan, and plan changes in Otago, Southland, Canterbury and Waikato, Mr Wills said.
Farmgate and commodity prices - last survey's most important issue - dropped to second place, while industry-specific issues were in third place, mainly about the meat industry sparked by poor prices for lambs.
The survey, undertaken at the start of the 2013-14 season, showed a ''major'' turnaround in farmer confidence, in keeping with other recent farm and business confidence surveys.
While last season's drought would make the new season a challenging one for many, farmers were entering it with a lot more optimism in both the wider economy and individual farm prospects, Mr Wills said.
Dairy farmers remained the most optimistic industry group, which was not surprising given payout forecasts and expectations of a recovery in production, he said.
It was especially pleasing to see sheep and beef farmers feeling more optimistic - ''admittedly, this comes off a low base following a very tough 2012-13 season'' - but the gap in sentiment between dairy and the rest of farming remained large.
That set a strategic work programme for Federated Farmers, especially as it related to red meat and fibre.
While some progress was being made with wool, the red meat sector ''desperately'' needed reform and both farmers and the industry understood that need, he said. Efforts were being made to drive change in the industry with the formation of the Meat Industry Excellence group and discussions among meat companies.
''For many farmers, change cannot come soon enough, but for some it is already too late as they consider changing land use to dairy or forestry or even exiting farming altogether,'' the survey said.
The highest priority remained the Government's fiscal policy - reducing government spending, ''balancing the books'' and reducing government debt.
Farmers were more positive about their own profitability for the coming year than they had been at any time over the past two years.