Under the plans, announced Thursday, subsidies for private storage of cream and skimmed milk powder would be abolished and an EU-wide quality standard for butter would be introduced.
The Commission also wants to open up school milk subsidies to semi-skimmed and skimmed milk, reflecting consumer trends towards lower fat dairy products.
The move represents the first ripple of reform across the EU dairy sector, ahead of the Commission's comprehensive dairy review next year.
It is hoped the mini-reforms will go through within six months.
Dairy is a vital part of Europe's income from agriculture.
Milk makes up 14 per cent of EU agricultural output and annual turnover in the dairy processing sector is around €117bn.
Mariann Fischer Boel, agriculture commissioner, said of the proposed shake-up: "The proposed changes will continue our ongoing exercise of simplification, which is very important to me."
She gave special support to the reform of school milk subsidies.
The plan would see subsidies de-coupled from fat content in the milk, and so open up more money to lower fat milk.
"This will allow us to reflect changing consumer preferences and give more freedom to the Member States to decide how to organise the scheme on a national level."
The Commission said it would also grant the dairy industry's wish that EU rules on protein content for milk powder should match those set internationally by Codex.
Other changes anticipated are an end to milk subsidies for the military, a set intervention scheme for butter that would automatically run from March to August every year, and more freedom for dairy firms to choose the fat content of their milk – as long as levels are labelled on packs.
Joop Kleibeuker, secretary general of the European Dairy Association, welcomed many of the Commission's proposals, particularly on school milk, butter intervention and milk powder protein levels.
But, he told DairyReporter.com
the EDA had reservations about scrapping subsidies for private storage for skimmed milk powder.
"Even though this has not been used for many years, it may be that private storage will be a good instrument to help dairy firms cope with oversupplies in the summer and shortages in the winter
[as market support is reduced]."