Mamasadyik Bakirov, governor of Osh State, was driven away when he tried to talk to demonstrators.
On Wednesday, police opened fire on thousands of protesters attempting to force their way into the presidential palace.
The interim government's health minister said 74 people had been killed and 530 others injured in the unrest.
The unrest followed unrest Tuesday in the northern Kyrgyz town of Talas, during which at least 15 police officers went missing and 16 civilians and 85 policemen were injured.
The uprising broke out after the head and deputy head of the main opposition Ata-Meken party were arrested Tuesday.