The move gives the Irish presidency a mandate to negotiate the final deal with the European Parliament and was cautiously welcomed by Scotland's Rural Affairs Secretary, Richard Lochhead.
However a failure to bring in a level playing field on coupled payments to help the Scottish livestock sector "tainted" the deal for Scotland, he said.
Mr Lochhead fears the proposed two-tier system will leave Scotland unable to spend more than 7%, compared to 12% on offer to other nations.
"I sincerely hope this is one area which can be addressed in the negotiations between the European Parliament and the Presidency. The European Parliament has adopted a much fairer position on this and I hope this matter can be addressed," he said.
NFU Scotland president Nigel Miller broadly welcomed the agreement saying: "The concerns we had for Scottish livestock farms have in most cases been resolved, but there are still serious worries about the extent to which most arable farmers will be hampered.
"The reduction of the ecological focus area to 5% is welcome, as is the agreement to permit equivalent greening measures as an alternative option to the three greening measures, but the impact of the crop diversification rules remain significant for many cereal farms."
Another key point of the deal for Scotland was providing support for new entrants and topping up the support available to some recent new entrants, but the mechanism to win support for future new entrants has not been agreed.
The board of directors of Lawrie & Symington has appointed Brian Dickie as chairman of the Lawrie & Symington Group. The appointment follows Michael Clark's recent resignation.
Mr Dickie, who is 59 and has an extensive hill farming business based at Spango Farm, Sanquhar, Dumfriesshire, has been a member of the board of directors for the past three years.
Lawrie & Symington sold 323 store cattle in Lanark on Tuesday to a top of 285.7p per kg and an average of 238.9p, while 264 store heifers peaked at 258.3p and levelled at 215.4p.
Craig Wilson sold 1482 prime hoggs, that included 700 Blackfaces, in Newton Stewart yesterday to a top of £105 per head and 242.3p per kg to average 195.7p.
The 230 cast sheep forward saw ewes sell to £87 for Beltex and £52 for Blackfaces.
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