Lawyers in Turkey's third city, Izmir, have filed a complaint against the country's most senior military officer.
Thousands of Turks have been demonstrating in support of the flag
The complaint says comments made by Gen Hilmi Ozkok, after two young Kurdish men tried to burn a Turkish flag, created hatred between citizens.
He had described the men, who tried to burn the flag during a Kurdish festival a week ago, as "so-called citizens".
The incident provoked a week of demonstrations across Turkey in support of the Turkish flag.
The general's irritation at the incident in Mersin, in south-eastern Turkey, was clearly shared by much of the population, in some part whipped up by the nationalistic media and by state organisations, says the BBC's Jonny Dymond in Istanbul.
Turkish flags have been fluttering from cars and buses, office blocks and homes in a way that is normally reserved for public holidays.
Kurds make up about a fifth of the Turkish population.
They have regularly been punished for attempting to assert their separate cultural identity.
As part of its legal complaint, the Izmir bar association also lists more than a dozen incidents of nationalist threats and violence.
The move is, if not unprecedented, then certainly surprising, our correspondent says.
The military is no longer the power it once was, but it is still a respected, and to some degree untouchable institution.