"There are 311 soldiers including 9 generals who are on the run," Isik told CNN Turk television network, adding that efforts were underway to find the soldiers.
Isik also commented on the closure of military schools as part of a series of key decisions made in the aftermath of the deadly coup attempt, which martyred more than 230 people and injured nearly 2,200 others.
The minister said the decision would affect 3,900 students.
"These schools are used as strongholds of FETO terrorist organization. We have carried out technical analyses. The Measuring, Selection and Placement Center [OSYM] started administering the military school entrance exam in 2000. The exam questions between 2000-2014 were all leaked," he said.
Isik added that the technical analyses also revealed that over 95 percent of the current military school students "are in connection with FETO".
Under a statutory decree announced on Monday, Turkey's land, naval, and air forces are now placed under control of the Defense Ministry, while Turkish Coast Guard and Gendarmerie General Command have been brought under the control of the Interior Ministry.
The move allows the president and the prime minister to receive information directly from the force commanders when it is necessary and to give them direct orders, which will be fulfilled immediately without approval from any authority.
The decree also closes all of Turkey’s war academies, military high schools, and high schools that train non-commissioned officers, to be replaced by a new university called the National Defense University under the Defense Ministry.
The university will offer new institutions to train staff officers and give postgraduate education, including war academies and vocational schools that train non-commissioned officers.
The decree also assigns Ankara's Gulhane Military Medical Academy and military hospitals across Turkey under the Health Ministry. Health service priorities will be given to the relatives of martyrs and veterans.
A total of 3,073 military personnel including 158 general and admirals have been dismissed from Turkish Armed Forces over links to Fetullah Terrorist Organization (FETO).