The building "has been completely freed of separatists" Arsen Avakov wrote on his Facebook page. "Thanks to all those who offered their help," he wrote, without specifying how the protesters were removed from the building.
Activists yesterday shouting "Russia!" broke through police lines and stormed several government buildings in eastern Ukrainian regions seeking independence from Kiev following last month's fall of a pro-Kremlin regime.
In addition to Kharkiv, the protesters had taken over state buildings in Donetsk and Lugansk.
The unrest also came with Ukraine's borders surrounded by Russian troops who had earlier seized the Black Sea peninsula of Crimea and the economy in tatters after decades of mismanagement and government theft.
Several eastern regions now want to stage referendums on joining Kremlin rule when Ukraine holds snap presidential polls on May 25.