CONTRADICTIONS and conflict between the military on the one hand and the political government and judiciary on the other are unavoidable in this transition to a fully democratic constitutional state. This is because both the military and these civilian institutions have differing notions regarding this transition. So, even though they are necessary and unavoidable, the manner in which these contradictions and conflicts are handled and resolved will determine the fate of the transition.

Recently, such a conflict between the military and civilian institutions took a dangerous turn. For the first time in Pakistan`s history, the defence minister, under his own signature, has registered an FIR against a member of the armed forces and unknown others for engaging in the practice of `enforced disappearances` The Supreme Court in the Muhabbat Shah case has labelled this a crime agalnst humanity under international law. In other words, the defence minister has become a complainant against his own ministry of defence.

Facts: The human rights case was initiated by Muhabbat Shah for the recovery of his missing brother Yaseen Shah. The case took a dramatic turn when the superintendent of the judicial lockup, Malakand, informed the SC last year that in the now infamous case,`35 missing persons`, including Yaseen Shah, were illegally taken away by the army authorities from his internment custody in 2011.This was a categorical admission by a civilian state official and it was confirmed when the military produced some of these missing persons before the SC. In the presence of this admission and the known facts, the SC, through its judgement of Dec 10, 2013, declared that the military had engaged in the practice of enforced disappearances. But the court also showed a way out of this crisis.

Firstly, the production of these persons was made the responsibility of the prime minister and the KP governor.

Secondly, the court said that the persons responsible for the illegal detention `should be dealt with strictly in accordance with the law`. Let me re-emphasise here that the SC left it to the federal government to select its legal path of holding people responsible.

More importantly, there is no subsequent order directing either the defence ministry or the defence minister to become complainants themselves in such an FIR.

Thirdly, the court instructed the government to initiate a law to stop enforced disappearances.

The civilian view: With around 721 missing persons cases pending in the superior courts, the non-compliance with the SC`s repeated orders and its inability to provide even basic relief to ensure the release of the detainees, the frustration of the top judiciary is understandable.

The frustration of the civilian government is also understandable. The reasoning goes:`We didn`t create this missing persons problem but are blamed for not solving it. We neither have the custody of such missing persons nor do we know their whereabouts, but we are expected to produce them.

It is this frustration building up for many years, and a genuine desire for an early solution which has led to this present conflict with the military.

The military view: The basic frustration of the military is simple: `No one understands the difficult circumstances in which we work, nor is anyone willing to listen to our viewpoint on the missing persons issue.` The military`s frustration is also understandable because the initial steps towards solving any problem are to understand its causes and to see whether the key actors have a desire to resolve it.

The missing persons` issue, in relation to Islamist militants, has two basic causes.

Firstly, the Musharraf government initiated and encouraged such practices with no checks. Secondly, as the military perceives it, there was no legal system of long-term detention laws in Pakistan (as in the Guantanamo Bay system) fulfilling the requirements of the military. There was also a lack of convictions of suspected terrorists by the criminal courts.

Moreover, the military has shown that it is now also part of the solution by facilitating the recovery of many missing persons, a dramatic reduction in the number of the latter in the last couple of years and the military`s will-ingness to have a law on enforced disappearances, based on the recommendations of the Federal Task Force on Missing Persons.

On March 18, 2014, facing a scenario in which the SC could issue notices to the prime minister and KP governor for contempt in the 35 missing persons case, the federation`s legal team panicked. Someone wrongly advised the defence minister that he had to be a complainant in the FIR. This is wrong, because FIRs in missing persons cases are initiated by the relatives of the `disappeared`.

Secondly, the federal government has itself formed a judicial commission to look into this issue and filed a review in the Muhabbat Shah case. But by registering the FIR, it has damaged the defence of the defence ministry before the SC. In short, the FIR could, and should, have been registered by the relatives of the missing persons.

Bad legal advice resulting from panic has led to this crisis. It needs to be corrected. Also there is an immediate need to enact a completely new legal framework on enforced disappearances and not merely (ineffective) amendments such as the Protection of Pakistan (Amendment) Ordinance, 2004.

Perceptions are important and the perception of a defence ministry registering an FIR against itself can seriously damage this fragile transition to constitutional democracy. • The writer is a former member of the Federal Task Force on Missing Persons.