Workers using heavy digging equipment began excavating sites near a military facility in Silopi. Two pieces of bones have so far been found, lawyers say.
Last month, prosecutors ordered the digs after receiving requests from the families of dozens of missing Kurds.
The alleged killings took place during a Kurdish campaign for independence.
The Kurdistan Workers’ Party (PKK) has been fighting for an independent state since the 1980s, since when close to 40,000 people have been killed.
During the conflict, which reached a peak in the mid-1990s, thousands of villages were destroyed in the largely Kurdish south-east and east, and hundreds of Kurdish civilians disappeared.
" We believe much more could have been found, if we’d been given access immediately "
Rojhat Dilsiz
Lawyer for families of missing Kurds
Lawyers for more than 70 families applied to the prosecutor’s office in Silopi after information emerged suggesting the location of their missing relatives’ bodies.
A former security forces officer, now in hiding abroad, gave information about the torture and execution of Kurdish civilians.
The families were also boosted by the unprecedented arrest of members of the Turkish military, retired and active, in connection with an alleged plot to topple the government. Several of those in custody were in command in the region in the 1990s.
The prosecutor subsequently ordered the excavation of five sites, including two old well-shafts behind the abandoned Sinan roadside restaurant and a storage facility of the state Botas Petroleum Pipeline Corporation.
Lawyers also want to examine parts of a municipal cemetery, where they believe a mass grave of the missing could be found.
‘Suspicious’ location
Monday’s excavations on land owned by Botas, which lies in a restricted military area, focused on a "hollow and suspicious" location close to a military police building, one of the lawyers told the BBC.
Two pieces of bone and bits of cloth were discovered, they said, adding that some of the pieces of cloth had black spots on them, possibly blood stains.
All the evidence has been sent to a laboratory for analysis.
Another lawyer from Silopi, Rojhat Dilsiz, told the BBC that they had hoped to find more at the Botas facility.
"We applied for permission to dig at the start of December. Now it’s March," he said.
"We believe much more could have been found, if we’d been given access immediately," he added.
The excavations will continue on Tuesday at a second site, behind the Sinan restaurant, where three bodies were found in 1993.
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