One of the important lessons taught by the study of  military dictatorships is that when the military rules as an institution, such as in the case of the military-bureaaucratic regimes of Southern Europe, Latin America and East Asia in the 1960s through the 1980s, organisational professionalism is compromised. Having military officers sitting at desks as Ministers and department chiefs of non-military portfolios keeps them away from the training grounds and deployments in which military leadership is honed and exercised. Having soldiers patrol the streets and suppressing domestic dissent takes them away from the combat tasks that are supposedly their reason for being. Prolonged tenure in government makes both officers and enlisted personnel susceptible to the temptations of unchecked authority, from material corruption to unethical personal behaviour.
The very nature of military organisation is incompatible with governance. Whether it be collegial or Prussian style or some variant thereof, the military is a pyramidal organisation in which orders are passed from top to bottom and duties are delegated without question. There is no cabinet made up of ministerial equals. Instead, there is either one Military Commander or there is a High Command or Joint Staff comprised of similarly ranked chiefs of different armed service branches, and even then there is a first amongst equals. The further down the chain of command the more immediate and tight the degree of control of superiors over subordinates.
The rationale underpinning the organisational ethos and structure is to promote discipline under fire. There is little room for compromise and stakeholder consultation such as that which is the norm for most public agencies. There is no public consultation and few feedback loops other than after action reports and what soldiers tell their superiors in a chain of command. Superimposing a military organisation on the State apparatus may impose discipline (or at least fear) on the public bureaucracy, but the price paid for that is the softening of the military organisation in question.
The situation is compounded by militaries that use foreign peacekeeping missions as a substitute for combat exercises and as a source of remittances (since UN pay tends to be much high than local military pay in most of the world). Whatever dangers exist in peacekeeping, and there are many, keeping the peace is not, nor can it ever be, a substitute for combat training.
When taken together these factors erode the professional competence of the military as an institution. In countries that have military rule and conflicts with neighbours, this is often seen as a sign of weakness by adversaries. After all, pushing pencils and having long working lunches is not quite living like in a tent eating rations in between live fire exercises. Thus, somewhat ironically, prolonged military rule invites attack by hostile states in which the military does not rule and instead focuses on its combat role.
The capture of 45 Fijian Army peacekeepers in the Golan Heights by the Al-Nusra Front is a variant on this theme. The Fijians were part of a detachment that included a similar number of Filipino soldiers. When the al-Nusra rebels surrounded and attacked their jointly held UN outpost, the Filipinos, who have years of experience fighting Abu Sayyaf  rebels in the southern Philippines,  staged an armed retreat that allowed all of them to escape capture. They laid down suppressing fire as they drove their armoured column out of the compound at speed, and prevailed in the firefight occasioned by their escape. They suffered no losses.
The Fijians, on the other hand, although being similarly armed and equipped, surrendered without a shot. They are now waiting “divine justice” at the hands of their al-Nusra captors. Neither the Fijian military nor the military government can do anything about the situation, and instead have to reply on UN negotiators for the safe return of their soldiers. Other than appeals to the captors, the only response evident in Fiji is threats to the local Muslim community made by some Fijian nationalists.
The difference between the two outcomes in the Golan Heights is attributable to relative military professionalism. The Philippines Army does not govern and fights on a regular basis with the Abu Sayyaf rebels. They are battle hardened and disciplined as a result. The Fijian Army, in contrast, has ruled Fiji since 2006. Senior military leaders from the rank of major up have held managerial positions in the civilian administration, and the military spends most of its time engaged in domestic repression rather than training for combat. As part of the sanctions levels against it, Fijian military officers were denied admittance to Western military colleges and the Fijian military does not participate in multinational exercises. In spite of a limited military exchange program with China, the Fijian military has not engaged in the types of corporate training that makes for an effective fighting force against other armed adversaries. Instead, it has sent hundreds of soldiers on UN peacekeeping missions, but this is more due to the domestic importance of remittances from Fijian soldiers to their kin (especially in the villages) rather than securing the benefits of operational experience in conflict zones.
The result is that what used to be considered one of the more professional military organisations in the South Pacific is no longer capable of defending itself when attacked by irregular forces abroad. It lacks the leadership and discipline required to engage in organised violence against such armed opponents because it has spent too much time focused on ruling rather than serving its compatriots.
All of this illustrates the point that, beyond the negative impacts of military rule on society at large, the military as an institution is adversely affected by military rule. This is why “enlightened” militaries that stage coups try to relinquish direct control of government as quickly as they can. But others, perhaps safe in the knowledge that they have no immediate adversaries and enjoying the perks of governance, tend to linger in power. In spite of their lofty nation building rhetoric, the longer they retain power the more likely that the military will begin to lose the combat leadership and soldiering skills essential for survival in battle. And should that military ever find itself in battle, it stands a poor chance of victory when confronting hardened soldiers.
That has been proven sadly true for the Fijian Army in the Golan Heights.