Osh has been at the centre of the intense fighting between Kyrgyz and a minority Uzbek population that forced tens of thousands of people to flee their homes.
Roza Otunbayeva, Kyrgyzstan's interim president, has said up to 2,000 people may have been killed in the violence.
Investigators on Saturday began exhuming some of the bodies of those killed in the clashes that were not officially identified before being buried.
Bakyt Alynbayev, the acting deputy interior minster, said the investigation was "in the interests of the victims themselves" and "necessary for settling the issue of compensation".
The violence in June followed an uprising last April that led to the overthrow of Kurmanbek Bakiyev as president and the installation of the provisional government.
Uzbeks and Kyrgyz in the north mostly supported the interim government, while Kyrgyz in the south largely backed Bakiyev.
Government officials accuse Bakiyev supporters of instigating this month's violence in an attempt to scuttle the referendum.
Al Jazeera's Clayton Swisher, reporting from the capital Bishkek, said almost a million people have been impacted by the violence.
"There's a lot of people who won't be able to participate [in the referendum]," he said.
"That will only further the sense of disenfranchisement amongst the southerners in this country, in particular, the ethnic Uzbeks who want more of a voice from their central government."
The proposed constitution would make Kyrgyzstan Central Asia's first parliamentary republic.