The agency must relocate due to the U.K.'s decision to withdraw from the European Union (EU). The EMA has been based in London since the agency was established in 1995.
Delegates from the 27 EU member states voted on the new location and selected Amsterdam.
"Amsterdam ticks many of our boxes," EMA Executive Director Guido Rasi said in a statement. "It offers excellent connectivity and a building that can be shaped according to our needs. I am very grateful that the member states took into account our requirements for business continuity and gave priority to the protection of public and animal health."
According to an internal survey, a majority of the EMA's 900 staff members would be willing to move with the agency to Amsterdam.
EMA and the Netherlands will jump-start their collaboration by establishing a joint governance structure to steer and oversee the relocation project, according to the agency. Early next month, the agency will make available a monitoring chart on its website that will allow visitors to track the progress of the relocation, according to the EMA.
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