While there are numerous smaller intelligence and investigating agencies, like Rangers Intelligence, Air Force Intelligence, Naval Intelligence, Special Branch, CID, FIA, etc -the big three, Inter Services Intelligence (ISI), Military Intelligence (MI) and Intelligence Bureau (IB), are at the forefront as far as "intel operations" are concerned in Pakistan and aboard. The job description of the big three intelligence organisations are pretty clear where the ISI in principle looks after the foreign threats; MI looks after the military related affairs and the IB looks after the internal affairs - but these three intelligence agencies seems to be out of control and "often cross the lines and even step on each other's toes", a former top intelligence official confirmed to Daily Times. In fact, according to Brigadier (r) Shaukat Qadir, former vice president and founder of the Islamabad Policy Research Institute (IPRI), "the ISI, at least under Gen Mehmood in 2000-2001, completely went out of control until he was sacked. It was more of an ego problem, where Gen Mehmood, the ISI director general, considered himself unaccountable." A trend which shows that it's not the institution but often its personnel which goes freelance for which various intelligence agencies have made there "counter-intelligence" units more stronger for better vigilance of their own operatives.

The civilian-military distrust could also be witnessed in the intelligence community where it is part of the book by the uniformed intelligence agencies, the Military Intelligence and the ISI to seals off the K-Block or the IB's Headquarters as a routine whenever there's a coup which shows a thread of animosity and mistrust between the civilian and military institutions. The politicisation of the intelligence agencies could be judged with the fact that at least 4,000-5,000 sacked Intelligence Bureau officials, who were previously profiled to be "unfit for service" due to political connections, were reinstated by the Pakistan People's Party (PPP) government with back pays and benefits only recently. The IB often accuses other intelligence agencies of interfering in its affairs - remember only in recent years more IB operatives have gone down than anyone else. So, how do our intelligence agencies work? They send out a daily report to the president and the prime minister via COAS, titled "eyes only" mostly "googled stuff" and constantly plays up threat levels apart from nagging for more funds. While the three big intelligence agencies have received all the latest tech and surveillance equipment from the United States, including serious investments in a new field, quantum computing to break terrorist codes, it is the human intelligence which the Pakistani intelligence agencies normally rely upon but lacks training in. "They work like sub-inspectors and mostly tap phones and chase people," confirmed a former intelligence operative. The incompetence of our intelligence agencies could be judged from the fact that they have completely failed to stop or pre-empt at least 87 percent of terrorist related crimes despite millions of dollars of funding and investment by the GoP and other allies in Pakistani intelligence network. The CIA's former operative Jonathan Hugh confirmed to Daily Times that the CIA had only recently secured around $500 million under a covert programme to give out "carrots" to the ISI for catching top wanted terrorists. The funding, part of the intelligence agencies, is also dubious and deliberately kept murky, one example of which is how General (r) Pervez Musharraf gave out a record allocation of Rs 2.2 billion and Rs 140 million to a premier intelligence agency from the Finance Ministry funds in November 10, 2007 in an effort to manipulate the elections which were to be held in 2008. Mostly a "secret fund" is also abused for funding various operations with no records available.

There's also a psychological warfare unit and press-handlers operated by various intelligence agencies through which they unleash targeted propaganda and plant stories through journalists on agencies' payroll. Certain top journalists had only recently received plots and houses via the new Younas Habib of the intelligence agencies, a notorious builder and developer from Islamabad known to be close to all politicians. Only recently, news planted by an intelligence agency made sure that Qari Saifullah backed by another intelligence agency was victimised and re-arrested on the basis of the story filed. Intelligence coordination is an area which Pakistan lacks and is regarded as the prime reason why our intelligence agencies had failed. As of now, there is no practical mechanism to actually exchange information between various intelligence agencies and although the government had set up the National Counter Terrorism Authority (NCTA), now headed by Zafarullah Khan, has "fallen to the dogs" according to the sources and is practically non-functional. A top intelligence chief confirmed to Daily Times that "we need an effective and efficient institution for collection of data, assets and monitoring of activities of all national, defence and domestic intelligence organisations - right now it's not working out well for us."