The conflict started last year when the politicians in Nepal started debating the integration of the former Maoist guerrillas , popularly known as People’s Liberation Army (PLA) into the country’s national army (NA). It was predicted then that the process could affect the structure and stability of the national army.
Dr. Divas at ABC reported  in January 2009 about a conflict between Defense Minister Ram Bahadur Thapa Badal and the national army Chief Rookmangud Katwal :
Badal and Katwal are at loggerheads over whether the NA should continue with fresh inductions to fulfill the vacant posts in the army. While Badal accuses the Army of trying to control a democratically elected government by refusing its directives, Katwal sounds defiance against the Maoists tactic of keeping the National Army under the Party’s control.
Katwal finds the Maoists ungrateful toward the NA in general and the Maoists find Katwal a major impediment against implementing their agenda. Since then the situation has degraded. Dr. Divas updates on April 23rd on the same post:
Prachanda supported a decision by the defense ministry two days ago to seek clarification from General Katawal over allegations that he ignored government orders on recruitment and the sacking of eight senior army generals.
Neil's Nepal warned of consequences :
The Army has been blatantly violating the principle of civilian control. [..] Not only this, the major opposition party is supporting the army in it’s continual violation, and the Maoists are probably not at the hight of popularity. Now that the Maoists are calling the army chief in for a “clarification,” something that could be a preliminary stage of sacking him, all traditional indicators would be pointing to an army coup. This is a particularly serious concern in light of the fact that the last army coup was a mere four years ago.
But the blogger also provided logic why the coup would not happen:
The PLA is still sitting out in cantonments, it still has it’s arms, and it’s still loyal to the Maoist chain of command. The army chief knows that if he uses some pretext to sack the elected government, he won’t just have to deal with an extremely organized street protest/urban uprising (from a party that is now entrenched in urban areas and highly militant). He’ll immediately have to pit his troops (who may not be so willing) against an 18,000 strong, highly motivated, guerrilla force.
United We Blog! for a Democratic Nepal informs  today that some “Generals of Nepal Army had made plans of (a) ’soft coup’ to tackle Maoist’s plan to dismiss the Chief of the Army Staff General Rookmangud Katwal.” Dr. Divas also updates  that General Katwal was for executing something within statute, a “Bangladesh-inspired President’s Rule backed by India Government”.
A detailed report has been published in eKantipur.com . It shows that Maoists were planning to integrate all 19,000 former guerrillas (PLA) in the National Army and several PLA commanders would get higher positions.
United We Blog! also posted the army's response strongly refuting the reports as “imaginary and illusionary.”
Neil's Nepal points  to the Maoists’ advantage:
The Maoists have found their way around this inconvenient fact by forming their own army (through great difficulty) and breaking the governments monopoly on the use of force. Hence, they don’t have the loyalty of the army (at least not the leadership), but they probably aren’t going anywhere anytime soon.