"The planned measures for Merck Serono's operations in Switzerland are needed to ensure our global competitive position in a rapidly changing market and to secure the long-term future of the company," said Stefan Oschmann, head of the Serono division.
"Regrettably, these planned measures include the closure of our headquarters in Geneva, which would result in workforce reductions and the redeployment of certain Switzerland-based functions to other Merck locations," he added.
The company said it planned to start retrenchments and relocations in the second half of 2012, and complete the closure of the Geneva operation in the first half of 2013.
Merck Serono will now operate out of a single campus in Darmstadt, Germany, to eliminate "duplications of functions" at two European headquarters, Merck said.
Some research and development jobs would also be transferred to Boston and Beijing, it added.
Merck Serono is to keep its production facilities in the Swiss towns of Aubonne and Corsier-sur Vevey, but plans to cut 80 production jobs there as well.
The company said it will begin consultations with employees on April 25.
Merck Serono has 17,000 employees worldwide, with about 1,250 in Geneva.
Merck purchased the Swiss group Serono in 2006 for 16 billion Swiss francs (€13.3 billion).
Merck Serono specialises in medications to fight neuro-degenerative diseases, such as multiple sclerosis.
Shares in Merck KGaA showed a gain of 0.24 percent to €82.58 in midday trading on the Frankfurt stock exchange, which was 0.52 percent higher overall.
Last month, Merck announced that its 2011 earnings were hit by one-off charges and that tough economic conditions would weigh on profits this year and next.
The company's net profits last year fell by 2.3 percent to €617.5 million.