It includes the removal of payments for so-called "slipper farmers", who do not use land for agricultural purposes, measures to further support sheep farmers and beef producers, and a cap on direct farm payments.
Rural Affairs Secretary Richard Lochhead detailed how the new Common Agricultural Policy (CAP) - the EU system of subsidies for farmers - told MSPs the package would not please everyone.
He said: "Some farmers, who were disadvantaged under the old CAP, will finally move towards a level playing field. Others will see their payments go down."
Land with no agricultural activity will be removed from the payment regime, with sporting estates to be excluded from receiving direct farm payments unless they can prove they are a genuine farm business.
Basic direct farm payments will also be capped at about £400,000 per year after labour costs to address the issue of huge individual payments.
Mr Lochhead also announced a £45 million three-year beef improvement scheme, and a "coupled support scheme" for sheep producers.
Labour welcomed the measures to tackle slipper farming and sporting estates.
David Johnstone, chairman of Scottish Land & Estates, said: "Scottish farmers have been seeking clarity and now everyone will be able to start planning for the future with a little more certainty."