The civilians were demanding greater protection for minority Shiites amid a recent spate of attacks, including the twin blasts in Parachinar on June 23 in which more than 70 people were killed.
Army chief General Qamar Javed Bajwa ordered the probe during his visit to Parachinar where Shiite parties had organised sit-ins - against the attacks - for eight straight days.
In a meeting with a delegation of protesters, Bajwa promised to ramp up the security of the Khurram tribal region and announced several measures to this end.
"Every Pakistani is our brother. You are our strength. For me every Pakistani is equally important, even non- Muslims," he said.
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He also announced upgradation of the local school and hospital and promised to set up a trauma center.
The military's media wing said the government had already announced compensation for Parachinar victims at par with other such victims elsewhere in the country.
Army spokesman Major General Asif Ghafoor said Pakistan had already begun building a fence along its border with Afghanistan to combat cross-border movements of militants.
"In the first phase, sensitive locations on the border will be fenced; whereas in the second phase the rest of the border will be fenced," he said.
Parachinar, the headquarter of Kurram tribal district, is sensitive due to large Shiite Muslim population, living alongside Sunnis, who are in majority in Pakistan.