The counterintelligence service said in September that Russia was conducting "an information war" in the Czech Republic, building a network of puppet groups and propaganda agents that could be used to destabilize the country.
Chovanec said the ministry's new 20-member team will act to disperse misinformation in the public domain but also train public officials to be prepared to deal with disinformation.
"We want to get into every smartphone," Chovanec said at a conference on strategic communications which he attended alongside general Petr Pavel, head of NATO's military committee.
The center will need to be able to respond almost in real-time to various misinformation, using Facebook, Twitter and other means of communication, Chovanec said.
Kremlin officials were not immediately available for comment.
Dozens of websites in the Czech Republic, home to 30,000 Russians as of a 2011 census, promote Moscow's stance toward the West.
Chovanec said an opinion poll showed a quarter of people believe what they read on "alternative" news websites.
The Czech Republic has stuck to the common European Union stance toward Russia.
But a number of politicians - in particular president Milos Zeman - have echoed Russia's views on the situation in eastern Ukraine, including its insistence that no Russian troops are there, and spoken out against economic sanctions on Russia.