Photos courtesy of the BBC
Gen Yasar Buyukanit did not name those who were "trying to corrode the secular nature of the Turkish Republic".
His statement comes a day before MPs are expected to elect Abdullah Gul, a former Islamist, as president. His candidacy remains highly controversial.
The army sees itself as the guardian of Turkey's secularism. It has ousted four governments in the past 60 years.
This is the second warning issued by the army in recent months. Turkish army issues new warning (more)
Turkey awaits AKP’s next step By Sarah Rainsford
Mark Alexander