Ireland's designated lands are worth €2-3 billion - or between €1,000/ac and €1,500/ac - to the national economy each year, according to the EU Commission.
These benefits are provided in the form of direct farming output and in public goods such as bio-diversity, tourism and protection of carbon sinks.
The latest EU assessment has resulted in calls from the INHFA for a total re-evaluation of direct payments on these lands to farmers.
The Commission's Bio-diversity Strategy for 2030 estimates that Natura 2000 lands are worth €200-300 billion annually to the union's economy.
Given that Ireland has 1pc of the EU's total protected area, the country's share of the economic benefits from Natura 2000 equates to €2-3 billion a year, or €1,000-1,500/ac for the two million acres (800,000ha) of designated land in the state.
Reacting to the report, the INHFA claimed that the 30,000 Irish farmers with designated lands deserved a greater share of the benefits that accrue to the economy from these sites.
"Almost 10 years ago we were informed in Brussels that the EU valued the impact of designations at €150/ha/year. Up to this we have accepted that valuation, however, it may now be time to re-evaluate how everyone gets rewarded," an INHFA spokesman said.
The hill farmer body claimed that €50m from GLAS was the only environmental payment currently available to Natura farmers.
"The fact that these farmers must first join GLAS in order to receive any payment is unacceptable. In addition, the payment rate of €79/ha on a limited number of hectares has added injury to insult," he said.