The scheme to compel the land to be taken out of production, a process known as greening, is part of a proposed reform of the European Union's huge farm support programme, the Common Agricultural Policy (CAP).
The Commission has proposed payments to farmers linked to the adoption of measures that offer environmental benefits. These include maintaining an "ecological focus area" where crops would not be grown.
"It would be absurd to leave 7% of farmland fallow as an ecological focus area," Agriculture Minister Ilse Aigner told a news conference on Thursday (17 January) at the start of the Green Week food trade fair in Berlin.
Aigner said the Commission, the EU's executive arm, had verbally accepted objections that seven percent was too large an area but it kept the figure in its written proposals.
Negotiations on the new EU farm policy are due to end in June this year for a launch in 2014 but after delays in approving the EU budget, France expects a later start.
The Commission had shown itself ready to make compromises, Aigner said. Germany is pressing for certain types of environmentally-friendly land use to be counted in the 7% greening total.
European Union leaders were unable to reach agreement late last year on a budget for the 2014-2020 period, which has created uncertainty about the future level of farm spending.
Aigner said she expected negotiations on EU farm reform to be completed in summer this year and the budget talks to be finished in February.
EU leaders will resume the talks on the budget at a summit in Brussels on Feb. 7-8, officials said on Thursday.
Germany has been pressing for cuts in EU spending.