The move was announced over the fears that members of the anti-government organization known as the "parallel state" infiltrated Turkish authorities and tapped the conversations of the country's officials.
"The members of the 'parallel state' have infiltrated the strategic positions in the Scientific and Technological Research Council of Turkey, including the information security department. They knew the cipher system for old phones that they used for tapping. We have taken all necessary technical precautions and will distribute new phones with anti-tapping systems until the end of the year," Isik told journalists.
The parallel state is an organization linked to US-based Islamic scholar Fethullah Gulen. In September, 14 Turkish police officers were reportedly detained for their alleged connections with the organization, accused of infiltrating the state, wiretapping phone conversations and forging documents, among other felonies.
A wave of arrests has taken place in Turkey since 2013, with most of the charges linking the crimes to Gulen's targeting of Turkish President Recep Tayyip Erdogan, who has accused Gulen of attempting to overthrow his government through a series of protests in 2013.