In a formal letter, IB Director Asif Ibrahim said CBI's move to prosecute its officials in the alleged fake encounter case in Gujarat, would be "disastrous for the morale of IB officers" and would harm the country's internal security.
Sources said Mr Ibrahim wanted to put on record the IB's displeasure over the CBI's alleged attempt to frame its officers in the alleged encounter that took place nine years ago and wanted government action over it.
The IB has been maintaining that its officials only provided intelligence inputs and had nothing to do with any alleged fake encounter.
It has also said that the CBI does not have enough evidence to prosecute IB officers, including Rajendra Kumar, in the alleged fake encounter case. Mr Kumar was the Gujarat station chief of the IB when Ishrat and the others were shot dead.
The CBI has told a court in Ahmedabad that it would further investigate the role of four IB officials, including Mr Kumar, in the alleged fake encounter case.
IB's letter, received by the just retired Union Home Secretary RK Singh, has been forwarded to the Prime Minister's Office for further action.
The Ministry of Personnel, which is the nodal Ministry of CBI, falls under the direct jurisdiction of Prime Minister Manmohan Singh.