Benazir Bhutto appointed Rehman Malik as chief of the Federal Investigation Agency which then launched a secret war against the Islamists, which amounted to a direct attack on the ISI. The Pakistani military was equally dismayed by reports of FIA contacts with the Israeli secret service, the MOSSAD, to investigate Islamist terrorists. The FIA leadership under Bhutto also angered Islamist elements because they allowed the extradited Ramzi Yousaf to the US for trial on the New York Trade Centre Bombing. One of the first acts of President Leghari after dismissing Benazir Bhutto on 05 November 1996 was to imprison the Ghulam Asghar, head of FIA, suspended on non specified corruption charges, and Rehman Malik, Addl. Director General FIA, was also arrested.
The Federal Investigation Agency conducts the investigations on receiving reports of corruption, either through the P.M.'s Accountability and Coordination Cell or directly from the public. After the investigations, the cases are referred to the Chief Ehtesab Commissioner for trial by the Ehtesab courts. However, the Chief Ehtesab Commissioner, Mr Mujaddad Ali Mirza, has complained that the Federal Investigation Authority and the Anti-Corruption Police have failed to cooperate with the Commission.Police tactics in British India were never gentle, but in contemporary Pakistan, according to the Herald, a magazine published in Karachi, "The police have institutionalized torture to a point where it is viewed as the primary method of crime detention. Police torture has become so commonplace that it has slowly lost the capacity to shock and disgust." These charges were echoed by Amnesty International's especially bleak appraisal of Pakistan's human rights situation in its June 1992 "International News Release" report. The report, reflecting the law and order breakdown in Sindh and the government's reaction to it, stated that government opponents often are harassed, placed under arrest, and detained for unspecified periods of time. Scores of prisoners of conscience have been held for their political activities or religious beliefs. The practice of repeatedly bringing false charges against members of the political opposition is a widely used tactic in Pakistani politics and has been used to arrest thousands of opposition party activists. According to the United States State Department's Country Reports on Human Rights Practices for 1993, there were no significant efforts in 1992 or 1993 to reform either the police or the judicial system, and authorities continued to be lax in their prosecution of abuses in these areas. Pakistani and international human rights organizations have demanded that steps be taken to reverse the trend by bringing torturers to justice and by taking such procedural steps as reducing the time prisoners spend in places of first arrest, where most torture takes place. Torture is a particularly acute problem in cases in which the suspect is thought to have committed a political crime, but it is not uncommon in serious criminal cases. General police brutality in handling all suspects is routine. Police frequently act without warrants or other proper authorization, and individuals disappear into the criminal justice process for weeks before they can be found and, through writs of habeas corpus, be brought into regular judicial channels. Rape of prisoners, both male and female, is common. Prisoners often die in detention but are reported as killed in the course of armed encounters. Police also are alleged to extort money from families of prisoners under threat of ill treatment. The performance of the police and their failure to act against political groups that run their own torture machinery are especially bad in Sindh, but there is no Pakistani who looks on an encounter with the police with equanimity.