NEW DELHI: Intelligence Bureau (IB) chief Asif Ibrahim has formally complained to the home ministry against CBI , saying the investigating agency’s “witch-hunt” against its officials in the Ishrat Jahan case was “disastrous for the morale of IB officers” and would harm the country’s internal security.Ibrahim took the unprecedented step of putting on record his disapproval of the CBI investigation into the so-called “encounter” killing by writing a letter last week to former home secretary RK Singh, ET has learnt. Before that Ibrahim complained to National Security Advisor Shiv Shankar Menon on whose advice Singh is said to have intervened and called a meeting on June 13 of Ibrahim and CBI Director Ranjit Sinha to discuss the evidence available with CBI against IB Special Director Rajinder Kumar. However, after CBI did not relent at that meeting, Singh advised Ibrahim to put his objections on record in a letter rather than just as a verbal complaint, a top government source said.The IB chief ’s letter to the government made a case for ensuring some immunity for officers of a covert intelligence body and warned that to the extent of saying that CBI’s move to prosecute IB officers in the Ishrat Jahan case will be setting a bad precedent for counterterror operations and will be harmful for the internal security in the long run, the source, who is familiar with the letter’s contents, said. However, with CBI now putting the names of four senior IB officers in its chargesheet filed on Wednesday, Home Minister Sushil Kumar Shinde preferred to take a safe line. He said: “Facts are facts. Guilty should be punished.”But former IB chief Arun Bhagat said institutions such as the IB must be protected. “Individual faults may be there and the CBI must get to the bottom of it, but institutions like the IB have to be protected. The CBI should have come to a fair conclusion before making everything public as it does not help the image of the IB,” Bhagat said.A senior CBI officer said the agency had only done its job on the Gujarat HC’s orders to probe the fake encounter and exposed the “bad apples” in IB. Instead of blaming CBI, he advised IB to take lessons from the episode and frame standard operating procedures on how to conduct covert terror operations. “Let the IB go to the judiciary and seek immunity for themselves for counter-terror operations. We do not understand how IB’s morale will be affected by this… Hasn’t CBI arrested its own officers on charges of corruption in the past? Has that destroyed the CBI’s morale?” the top CBI official asked.