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In an interview with Russia’s independent Echo of Moscow radio station, Mayor Zdeněk Hřib confirmed that police had placed him under protection several weeks ago because of unspecified threats.
“By their decision, I am not able to comment on the reasons,” Hřib said.
The Czech weekly magazine Respekt, citing Czech intelligence, reported Sunday that a person carrying Russian diplomatic papers arrived in Prague three weeks ago to poison Hrib and Prague 6 District's Mayor Ondrej Kolar with ricin, a highly potent toxin.
The unconfirmed report drew fierce backlash from Russia. On Monday, the Russian Embassy in Prague formally protested to the Czech Foreign Ministry over the report.
"The allegations in the story are absolutely baseless" and designed to "discredit" Russia, the embassy said.
Czech authorities did not comment on the report.
Hrib and Kolar have both been strongly criticized recently by Russian officials. In February, a Prague square in front of the Russian Embassy was renamed after slain Russian opposition leader Boris Nemtsov, with Hrib unveiling the new nameplate.
In April, Kolar's district removed the statue of Soviet World War II commander Ivan Stepanovic Konev whose armies liberated Prague from Nazi occupation.
Prague 6 officials said the statue will be moved to a museum and a new monument honoring the city's liberation will be installed in its place.
The Associated Press contributed to this report.