The Russian president was fearful of a rerun of Nobel-prize-winning physicist Andrei Sakharov's farewell in 1989 which helped bring down the totalitarian Soviet Union.
State television and other media were ordered not to cover his most effective critic's funeral and most Russians have not heard claims that Putin ordered Mr Navalny's death.
The Russian special services were ordered by a worried Kremlin to carry out an "operation" to "protect the constitutional order from threats", the independent Moscow Times reported.
At least 45 people were arrested as thousands of defiant mourners attended the funeral of the late opposition leader yesterday.
The service took place in Moscow two weeks after Mr Navalny died aged 47 in an Arctic prison where he was serving a 30-year sentence.
His coffin was carried past a large crowd of attendees, some holding red flowers and who came in spite of fears the Kremlin would order mass arrests and send any young men present straight to the frontline in Ukraine.
Mr Navalny's parents sat with great dignity beside his open casket at the Mother of God Quench My Sorrows church on the outskirts of the capital.
Authorities wanted an anonymous farewell but Lyudmila Navalnaya insisted on this service for her son.
And, in spite of the heavy police presence, thousands chanted "Navalny" while others yelled "Putin is a killer" and "we will not forget".
Chanting
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