It said it had agreed the move with representatives of the 10,900 staff.
In February, the family-controlled company announced plans to cut costs across its businesses after setbacks in the marketing of two key drugs.
Merck said it would cut gradually. "The positions will be reduced in a socially acceptable manner," the company said.
It said it would focus on voluntary redundancies and early retirement programmes across all divisions and functions.
It was unable to bring out a multiple sclerosis drug and was also unable to widen sufficiently the use of its cancer drug, Erbitux.
Merck's cuts, which are part of what it calls its "fit for 2018" programme, will be accompanied by investment of 250m euros (Â£198m) in its site at Darmstadt and at other German facilities.
It said it would develop the Darmstadt site as the group's world headquarters.
German drugs and chemicals maker Merck KGaA plans to cut one in 10 jobs at its domestic sites by 2015 as part of a restructuring programme.