In an attempt to limit subsidies paid to large landowners, individual payments will be capped at £260,000 per year. Direct payments to some farmers, including vegetable growers will also be conditional on their taking around seven per cent of land out of production.
A joint statement from the NFU and the Country Land & Business Association described the proposals as disappointing and a missed opportunity.
"We would want the obligation to take up to seven per cent of a farm's area out of production significantly reduced. We also need to see the capping proposals that would discriminate against the UK rejected," it said.
However, the Soil Association welcomed the reforms, including those to CAP's Pillar 2 covering rural development.
In a statement, it said: "The proposed new separate measure for organic farming, designed to give organic farming greater visibility, is particularly important for UK organic farmers because we currently receive lower Pillar 2 payments in the UK than in any other EU member state.
"We expect this new proposal from the European Commission to deliver a degree of fairness to British organic farmers that they are currently denied."
The planned reforms make little impact to overall CAP levels, which will remain at more than EUR50bn, more than 40 per cent of the total EU budget, until 2020.
They must now be approved by EU governments and the European Parliament, which is likely to take up to two years.