"We are not satisfied with the current situation, and regard it as abnormal when the Czech authorities refuse to simplify the visa regime for Russians," Sergei Prikhodko told a news conference.
He said more than 200,000 Russians visit the Czech Republic every year, and that the Central European country could be more flexible with its visa regime.
At the same time, he said President Vladimir Putin was satisfied with his talks with the Czech leadership and commented that "there was no blatant fear of Russia, or clash of political forces over relations with Russia" in the country.
Putin's visit to the Czech Republic was the second leg of his east European tour, and the first time a Russian leader has paid an official visit in 13 years.