The sites were discovered last week when a shepherd came upon a fragment of human bone next to a small hill where his flock was grazing, said Abdel Hussein al-Hadi of the Centre for Martyrs, a religious non-governmental organisation in Nasiriyah.
Mr Hadi speculated that the bodies date from Saddam's suppression of the 1991 Shiite revolt.
There is no word yet on the number of bodies in the two graves, but a company specialized in excavating such sites has been contacted, Mr Hadi said.
Numerous mass graves have reportedly been found since Saddam Hussein’s regime came to an end, US officials believe there could be at least 300,000 bodies buried in mass graves across Iraq.