U.S. Secretary of State Condoleezza Rice and Czech Foreign Minister Karel Schwarzenberg signed the Status of Forces Agreement (SOFA) on Tuesday.
Defense Minister Vlasta Parkanova said the government had approved the final version of the agreement, which was coordinated with Washington last week. It has still to be ratified by the Czech parliament and signed by President Vaclav Klaus.
As part of the missile defense system, the United States plans to place interceptor missiles in Poland, but Washington has found it harder to come to an agreement with Warsaw.
The plans are fiercely opposed by Russia, which sees the missile defense shield as a threat to its national security and the system of international nuclear deterrence.
President Dmitry Medvedev has vowed to respond to the deployment of the U.S. missile shield in Central Europe.