Justice Mukhtar identified the practice as one of the reasons for undue delays in the criminal justice administration system in the country.
The CJN spoke at a special session organised by the Supreme Court to mark the commencement of the 2013/2014 Legal Year, as well as the inauguration of 17 new Senior Advocates of Nigeria in Abuja on Monday.
She frowned at the "unwholesome practice of some security agents involved in the criminal justice administration system," particularly the arraignment of suspects without first gathering evidence for prosecution.
"It is common knowledge that our security agencies usually rush to the courts with suspects, before looking for evidence to prosecute them.
"The persistent use of the 'Holden Charge' by these agencies to detain awaiting trial suspects, is a major contributor to the high number of cases pending in our courts," she said.
The CJN advised the security agencies to emulate the practice in other parts of the world, where adequate evidences were obtained before suspects were arrested and charged to court.
Admonishing the security agencies to adopt a more effective approach, she said, "This procedure is a far cry from what obtains in other democracies, where discrete surveillance is placed on crime suspects who are painstakingly stalked by security agents, until such a time when enough evidence would have been obtained for their arrest, arraignment and prosecution.
"But in Nigeria, suspects are promptly arrested and often times arraigned in court, even when no evidence for prosecution has been gathered.
"The backlash from such failure of proper investigation by our security agencies is the resultant hike in the number of cases pending in the courts."
Justice Mukhtar warned that "an extreme consequence of these glaring lapses may lie in the loss of confidence in our domestic justice administration system which rubbishes our often brandished favourable investment climate and translate to a huge disincentive to potential foreign investors in Nigeria."
She restated her call for an overhaul of the country's criminal laws, which she described as "archaic and culturally irrelevant."
The CJN further expressed concerns at the slow pace of administration of justice in the country.
"To exhaust complete remedy in a case, that is from trial court to Supreme Court, could take up to 20 years with the original litigants dead and substituted and in some cases the substitutes also dead and substituted," she said.
She added that the process of interlocutory appeals aggravates the situation to the extent that by the time the Supreme Court decides that they be continued in trial court, most of the witnesses might have died or alive but senile, with documents no longer traceable.
Justice Mukhtar also spoke on the challenges militating against her resolve to restore the fading glory of this country's judiciary.
She stressed that, for her to achieve the objective, "certain indices have to be guaranteed, for instance government must at all times ensure total compliance with the rule of law as well as adherence to the principle of separation of powers."
Speaking of the need for compliance with the principle of separation of powers, the CJN noted that the National Judicial Council had the exclusive powers to deal with policies relating to policy and administration in the judiciary.
Noting that, under a democratic dispensation, the three arms of government must keep faith with the doctrine of separation of powers as enshrined in the 1999 Constitution, she stressed that "the Judiciary must continue to defend its independence so that it should not merely be apparent but must be seen to be real."
"By virtue of Section 153 of the Constitution, the National Judicial Council is the apex body for the nation's Judiciary.
"By paragraph 21(1), part 1 of the Third Schedule of the 1999 Constitution, the Council has the power to deal with matters relating to broad issues of policy and administration of the Judiciary," she added.
Also speaking at the event, the President of the Nigerian Bar Association, Mr. Okey Wali, SAN, canvassed the inclusion of NBA's representatives in the NJC in disciplinary proceedings against judges.
Wali also spoke of heightened efforts by the NBA to address issues of indiscipline among legal practitioners.
He said seven lawyers were expelled from the bar in the past legal year after being indicted for various acts of misconduct, while two others were suspended.
The NBA President also echoed the CJN's concerns over the "poor funding" of the judiciary.
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