Foreign Minister Mohammad Javad Zarif's visit comes just six months after the head of Iran's nuclear program met Czech leaders in May to discuss developing bilateral nuclear cooperation.
Iran is seeking help from European nations to improve its civilian nuclear program. The Czechs heavily rely on nuclear energy and plan to build more reactors.
Zarif and Czech counterpart Lubomir Zaoralek gave no details after their meeting.
"It's a promising field," Zaoralek said about the nuclear cooperation. "There's an interest on both sides to cooperate."
Accompanied by a delegation of Iranian business leaders, Zarif was also to meet Prime Minister Bohuslav Sobotka and the speaker of Parliament's lower house, Jan Hamacek.
Last year's landmark nuclear deal between Iran and world powers lifted painful international sanctions in exchange for Iran curbing its nuclear activities. Iran has denied ever seeking atomic weapons, insisting its nuclear program is for purely civilian purposes.
"Iran has been implementing its part of the bargain," Zarif said. He claimed the United States has not fully implemented its part.
Zarif called it "a reasonable agreement, good for everybody. That's our preference... (but it) doesn't mean we do not have other options."
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