The Russian embassy in Prague requested police protection from one of its diplomats, who was appointed by the Czech media amid allegations of a conspiracy to poison Czech politicians.
He said "false and baseless" allegations were made against one of his employees and he was now receiving threats.
There was no confirmation that three Czech mayors were the focus of a plot.
But all three – including the mayor of the city of Prague – obtained police protection.
Last month, a Czech weekly, Respekt, claimed that a Russian agent had traveled to Prague with a suitcase containing the highly potent toxin, ricin. He suggested that the poison could be used to attack Czech politicians who angered Russia.
Who is the man called in the Czech media?
A Czech TV news report claimed that the reports involved Andrei Konchakov, head of the Russian Center for Science and Culture in Prague, and suggested that he was an undeclared intelligence officer.
Without naming him, the embassy said on its Facebook page that a member of its team was the target of an "anti-Russian information campaign" and that it was forced to request police protection for him. The diplomat said the diplomat was the victim of a "slander campaign" sparked by the Czech media.
Konchakov told the Czech website Seznam Zpravy that he brought "disinfectants and sweets" to the country in his suitcase, and did not ricin as claimed.
Several Russian media also reported his name. According to his biography on the website of the Russian center in Prague, he was born in 1986 and received his current job in December 2017.
The head of the federal agency for which he works in Moscow dismissed the reports as "pure provocation", linked to an ongoing dispute over the removal of a statue of Soviet Marshal Ivan Konev in Prague.
Prague and Moscow are due to start talks in the coming days to try to ease the growing tension in bilateral relations.
Who is Konchakov?
By Rob Cameron, BBC correspondent in Prague
Is Andrei Konchakov's cover blown up? Is he really an undercover agent?
Russia denies that which, even if it were, is understandable. That is the goal of being an undeclared intelligence agent.
The Czech authorities also do not comment. But in the past they complained about the oversized Russian diplomatic delegation.
In 2018, there were 121 Russian diplomats and support staff in Prague, and another 18 at the country's consulates in Brno and Karlovy Vary. It is one of the largest Russian diplomatic missions in Europe.
Exactly how many are spies using diplomatic cover is known only to Moscow. Czech authorities believe it could reach 40%.
Czech journalists are now tweeting pictures of Konchakov on his Facebook account. One of the most recent shows him surrounded by members of the Russian biker gang Night Wolves, in front of the statue of Russian WWII general Ivan Konev in Prague.
This is the statue that has now been removed; the act that caused so much anger in Moscow.
Who are the three mayors?
One of them is Ondrej Kolar, mayor of the sixth district of Prague, who ordered the removal of the statue of Marshal Konev. He hid when news of the plot surfaced and told the BBC that "the Czech police and secret service have information that there may be a threat directly from the Russian side".
The mayor of Prague, Zdenek Hrib, supported the renaming of a square next to the Russian embassy after Boris Nemtsov, an opposition leader assassinated near the Kremlin in 2015.
The third is another district mayor, Pavel Novotny, who supported a memorial to the anti-Soviet "Russian liberation army". Historians say the RLA, a division of Soviet prisoners of war integrated into the German army, has done more to liberate Prague than the Red Army, but Moscow sees them as fascist collaborators.