Gunfire broke out in Jalalabad on Friday, after angry protesters had seized government administration buildings and the city airport the previous day.
Violence was also reported from the cities of Osh and Batken, where protesters took over several government buildings.
A crowd of protesters also torched a house belonging to Bakiyev's brother, the interim government's chief
of staff said on Saturday.
The house, in Teyyit village near Jalal'abad, was almost
completely destroyed by the fire.
Our correspondent in Kyrgyzstan said: "We were there earlier to have a look and the damage was complete wanton and clearly retribution for what happened.
"We don't know precisely who lit it but we do know that a community leader was there with his people and he didn't deny it very hard. This doesn't say a lot about the control the interim government claims to have."
Interim authorities said Bakiyev, who fled the country after an uprising last month, was behind the unrest and said its organisers also "wanted to ignite an inter-ethnic conflict in the country".
"Bakiyev is behind all this," Omurbek Tekebayev, the deputy chairman of the interim government, said on state television.
The south of Kyrgyzstan was the power base of Bakiyev, who has now taken refuge in Belarus.
He was unseated in April after anti-government protests sparked clashes with security forces leaving at least 86 people dead.
Bakiyev had himself come to power in a popular uprising, the so-called Tulip Revolution of 2005, but became increasingly unpopular amid allegations of corruption and mismanagement.