Describing bugging as an unethical act, Atalay said that the government was determined to bring to light the truth over the claims.
On Monday, a paper linked to the government printed details of a private conversation held in the office of Onder Sav, the secretary general of the opposition Republican Peoples Party (CHP).
The CHP has alleged that members of the security forces had conducted the illegal bugging operation.
Atalay said he had ordered authorities to conduct a full investigation into the CHP claims. Bugging, which is illegal, harms personal freedom and violates human rights and liberties, cannot be approved, Atalay said during a press conference in Ankara.
Earlier Wednesday, Deniz Baykal, the chairman of CHP told a press conference that democratic rights ensured under the constitution had been violated by the security forces that had been tasked with protecting those very rights.