Alexander Vondra also said that plans by the U.S. Congress to restrict funding to build the system that would include a radar in his country and interceptors in Poland could deliver a blow to relations.
The Bush administration has argued that the system could extend the protection of a U.S. national missile defense system against a threat from Iran to Europe.
Vondra said that he believes that threat is real, but that hosting the U.S. radar would provide other security benefits.
"For us in the Czech Republic with our location between Germany and Russia, to have an installation with a few American soldiers is a good thing," he told an audience at the Heritage Foundation, a conservative think tank.
Russia has stridently objected to the building of the system, arguing that it could pose problems for its nuclear deterrent. But the United States has said the European system is aimed at countering the threat from Iran's ballistic missile program.
Vondra was meeting Bush administration officials during a two day visit as well as some lawmakers. Congress is nearing passage of a bill that would cut funding for the building of the site in Poland. The move could delay construction of the system.
Vondra said that he believes the system will eventually be built, but said that it would send a poor signal to his country, after his government has lobbied so hard for domestic approval of the project.
"You have to be serious with the allies," he told The Associated Press after the event. "We are fighting and investing a lot of capital."