Gen Yasar Buyukanit did not name those who were "trying to corrode the secular nature of the
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
This is the second warning issued by the army in recent months.
In April, it expressed its concern after Mr Gul - the ruling Islamist-rooted AK Party candidate - only marginally failed to gain enough support from MPs to become president in a first round.
The following stand-off between the AKP and secularist parties in parliament sparked a political crisis that led to early elections in July.
The AKP won those polls convincingly, and again nominated Mr Gul, currently the foreign minister, for the post of president.
Mr Gul - who has failed to gather enough votes in the first two rounds - is expected to be elected in the third round on Tuesday.
Mr Gul denies that, and has vowed to remain loyal to the country's secular constitution.
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Gen Yasar Buyukanit (archive)