One of the primary concerns of the regency was the constitution of those military mechanisms appropriate to a modern, Western-type state. Kapodistrias had also attempted something similar. He had tried to integrate the irregular troops into semi-regular military formations faithful to the central power. The failure of this attempt and the general involvement of the traditional armed forces in political disputes persuadeded the regency to form a regular army with a centralized structure which would be controlled exclusively by the central power. For this purpose decrees were issued (25th February-9th March and 2nd-14th March 1833) on:
a) the dissolution and regrouping of the practically non-existent regular army
b) the dissolution of the irregular formations from the period of the Revolution
c) the creation of ten skirmisher battalions.
The regular army would include the infantry, the cavalry, the artillery and the corps of engineers. Provision was also made for the introduction of armament, war tactics, hierarchy and the internal regulations of the European military systems, even for uniforms. Finally, the gap that would exist until the completion of the reformation of the regular army would be filled by 3,500 soldiers from German petty-states, as provided for by the Greek-Bavarian treaty of 20th October-1st November 1832.

These changes effectually excluded thousands of irregular troops from the military forces. The number of irregular troops is hard to determine and, according to the evidence of that time, it varied from five to thirteen thousand men. In theory, one part (2,000) could be occupied in the skirmisher battalions, which preserved many traditional elements (dress, tactics, armament) in order to become attractive to the traditional armed men. However, the introduction of internal regulations in the regular army, the dependence on the central power and the low salaries made only 35 veteran fighters join the skirmishers. The policy of exclusion in combination with the violent dissolution of the irregular troops by the Bavarian battalions provoked discontent among the armed men. A great number of them defected to the neighbouring Ottoman regions claiming the armatolikia of Epirus and Thessaly. Of those who remained within Greek territory many became bandits. In an attempt to reduce the constantly growing discontent of the military men the regency proceeded to found the Gendarmerie and Frontier Guard, which adopted the dress style, armament and war tactics which suggested those of the armed men of the pre-revolutionary period. A considerable number of veteran fighters were absorbed into these forces which recruited soldiers from each district with the intention of eliminating banditry and local revolts. In addition, the Phalanx was formed, a chiefly honourable force in the lists of which several thousand veteran chieftains were included.