The agreement to station the U.S. radar near the Brdy military base about 90 kilometers (55 miles) southwest of Prague was signed on July 8 by U.S. Secretary of State Condoleezza Rice and Czech Foreign Minister Karel Schwarzenberg.
"We are heading to Brussels to complain against our government, because it is planning to place a radar in the middle of Europe, which affects other European countries as well," the CTK news agency quoted Jan Neoral, mayor of Trokavec and a member of the League of Mayors Against the Radar, as saying.
Czech mayors from the Brdy area earlier sent a letter to U.S. president-elect Barack Obama asking him to abandon the Bush administration's missile defense plans for the Czech Republic.
According to recent public opinion polls, two-thirds of Czechs are against the deployment of the U.S. radar.
The radar is part of a missile shield system that would also include the deployment of 10 interceptor missiles in Poland. The U.S. says it needs the Central European shield to protect against attacks by "rogue states" such as Iran.
The plans are fiercely opposed by Russia, which sees the missile shield as a threat to its national security.
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