Thousands have gathered on a hillside near the south-east village of Uldudere on the Turkish border with Iraq, to mourn the 35 smugglers killed by Turkish military jets on Wednesday.
The civilians were mistaken for Kurdish rebel fighters with whom the state has been in conflict since 1984.
The funerals quickly took on a political tone. The coffins were draped in red, yellow and green, the colours associated with Kurdish identity, and the PKK rebel group.
Speaking after Friday prayers, Turkish President Abdullah Gul apologised for what had happened.
“All the information indicates the dead people are civilians,” he said. “For that we all, from the government and the military, are very sorry,” he said.
There were also large protests in Istanbul, with people shouting anti-government slogans and requesting that those responsible be sacked.
Turkish rights groups have called for a UN sponsored investigation into the incident.