General Bajwa made his remarks while visiting the family of 22-year-old Lieutenant Arsalan Alam who was killed when militant fired at his post from across the border in Afghanistan on Saturday.
"Hostile agencies from abroad are trying to destabilise our country," Bajwa said, but stopped short of naming any country.
"They (hostile agencies) fear the Army for being a hurdle to achieving their nefarious designs," Bajwa said.
This terminology was traditionally used for India but now Afghanistan's intelligence agencies are also branded as hostile.
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He said the Army will continue to work for defeating militants.
"Pakistan's enemy is our enemy. Use of force is the prerogative of the state alone," he said.
Relations between Pakistan and Afghanistan have been tense for months, with the two sides accusing each other of turning a "blind eye" towards certain militant outfits.
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