Kirill arrived in Kiev as part of a three-day visit to the country featuring liturgies in honor of the Baptism of Rus Day, RIA Novosti reported.
"Regrettably, people are trying to mar the patriarch's visit to Ukraine through these stunts," said Deacon Alexander Volkov, the head of the patriarch's press service.
The incident signals "a deep spiritual crisis in some social circles," he added.
The Orthodox Church in Ukraine split in the 1990s after the breakup of the Soviet Union. The Ukrainian Church of the Moscow Patriarchate is recognized worldwide, while the churches that split off are not, RIA Novosti reported.
Several dozen Ukrainian protesters gathered to protest the patriarch's visit near the presidential administration headquarters, holding banners reading: "Down with Moscow colonialist priest!," "For the united Orthodox Church centered in Kiev!" and "Down with Moscow occupants!"
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