"Compared to the past, the Turkish armed forces are continuing their struggle in a more conscious, determined and experienced manner," he asserted, calling for enhanced cooperation and coordination between state bodies as the only means to defeat the rebels.
"Separatist terrorist organisation" is the official phrase Turkey uses to describe the outlawed Kurdistan Workers' Party (PKK).
The PKK, blacklisted by the United States and the European Union, has been fighting the Turkish army since 1984 when its militants first took up arms in search of self-rule in Turkey's mainly Kurdish southeast.
The group, which has since dropped its demand for statehood, stepped up violence in recent months after calling off a five-year unilateral truce in June 2004 on grounds that Ankara's moves to expand Kurdish freedoms were insufficient.
Last week, the group announced a fresh one-month ceasefire until September 20 to give Ankara time to expand the rights of Turkey's Kurdish minority.
One of its demands was that the Turkish army stop security operations to hunt down PKK rebels.
The truce came after a landmark pledge by Turkish Prime Minister Recep Tayyip Erdogan to resolve the Kurdish problem with "more democracy".
Although the reports were never officially confirmed, the Turkish press widely suggested that Erdogan's pledge had raised eyebrows within the army as a move that deviates from official policy and one which could imply accepting the group as an interlocutor.