Kremlin spokesman Dmitry Peskov said Kallas was wanted for "desecration of historical memory".
Russian state agency TASS said the Baltic officials were accused of "destroying monuments to Soviet soldiers".
As well as Kallas, Estonian State Secretary Taimar Peterkop and Lithuanian Culture Minister Simonas Kairys were placed on the list, according to the ministry database.
Russian Foreign Ministry spokeswoman Maria Zakharova said: "This is only the beginning."
"Crimes against the memory of the world's liberators from Nazism and fascism must be prosecuted," Zakharova said.
A spokesperson for Kallas was not immediately available for comment.
A spokesperson for Lithuania's Kairys could not confirm the order to Reuters.
Baltic nations which were formerly part of the Soviet Union have announced plans to demolish Soviet-era monuments.
Kallas said in 2022 that Estonian authorities would dismantle 200 to 400 such monuments.
In response, the head of the Russian Investigative Committee, Alexander Bastrykin, ordered a criminal investigation into the matter.
The Baltic politicians risk being placed under arrest only if they cross the Russian border, otherwise declaring them wanted will have no real consequences.
Estonian and Lithuanian authorities have not commented on the latest development.
In total, Russia has put several dozen Baltic politicians of various levels on the wanted list - from municipal deputies of cities to members of national parliaments.
In addition, former Latvian interior minister Marija Golubeva was put on the list, the independent Russian media project Mediazona reported.
The interior ministry database does not specify under which article of the criminal code they are being prosecuted.
