Kamil Amin, from Iraq's Human Rights Ministry, said the work started on Monday on eight locations inside Tikrit's complex of presidential palaces, where much of the killing is believed to have taken place.
IS militants overran Saddam Hussein's hometown last June, capturing around 1,700 soldiers as they were trying to flee Camp Speicher, an air base previously used by US troops on the outskirt of Tikrit.
Later, the Islamic State group posted graphic images online that appeared to show its gunmen massacring scores of the soldiers after loading the captives onto flatbed trucks and then forcing them to lay face-down in a shallow ditch, their arms tied behind their backs.
Other videos showed masked gunmen bringing the soldiers to a bloodstained concrete river waterfront inside the presidential palaces complex in Tikrit, shooting them in the head and throwing them into the Tigris River.
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Their victory was helped by US-led coalition airstrikes, which were not initially part of the operation.
Amin told The Associated Press that at least 12 bodies were exhumed yesterday. Lab tests will be carried out to match them with DNA samples that have already been taken from families of around 85 percent of the victims.
Iraqi state TV showed forensic teams digging in an open area, helped by bulldozers as family members stood nearby. The bodies were tagged with yellow tags while weeping soldiers and relatives lit candles and laid flowers alongside the covered remains. One clip showed unearthed skeletal remains still wearing combat boots.