Congress leader Rashid Alvi on Friday quashed allegations that the enquiry ordered against former army chief General VK Singh was part of a political vendetta.
"Government will decide if inquiry will be conducted or not," Alvi said.
"People want to know if he (Singh) was doing it on his own or any political party was behind it," he added.
Meanwhile, reacting to reports, Samajwadi Party (SP) leader Naresh Agarwal said: "Government must stop people who have been at top positions from entering politics after retirement."
Media reports claimed that Singh set up a special unit in the army which tried to topple the Jammu and Kashmir government.
The report claims that a secret Board of Officers inquiry has recommended that the CBI look into the matter.
Media report also claims that the unit set up by Singh, called the Technical Services Division (TSD), a part of Military Intelligence, tried to block General Bikram Singh's promotion.
The reports said that the recommendation has been examined by the prime minister's office and the ministry of defence.
The report was prepared by director general military operations Lt Gen Vinod Bhatia as part of a Board of Officers (BOO) formed by Gen Bikram Singh to review the functioning of the top secret unit set up under his predecessor.