Ukraine's flag—with its horizontal bands of blue and yellow—briefly appeared late on Wednesday instead of the Russian white, blue and red tricolor on a screen located on one of Astana's main thoroughfares.
Putin was already in the city at the time, and the screen was soon switched off, but images and videos of the incident quickly circulated online.
The interior ministry said in a statement it was looking into all possible versions, including a technical glitch and a hacker attack.
According to an opinion poll conducted last year, a majority of Kazakhstanis are neutral regarding the Russia-Ukraine war, but among the rest, supporters of Ukraine significantly outnumber those of Russia.
And with Russia being one of Kazakhstan's biggest trading partners, issues in its economy often spill over. On Thursday, Kazakhstan's tenge currency fell to an all-time low against the U.S. dollar after a sharp weakening of the Russian rouble.
