The abolition of the three regional administrations was the most important decision taken during the proceedings of the Second National Assembly. This meant that the organs of the central administration would alone coordinate communication and actions between the rebellious regions. These organs now had real power. Thus, the different factions and groups of interests which functioned in the Revolution tried to control these organs. The Second National Assembly attested that the notables of the Morea (Lontos, Zaimis, Sisinis, Deligiannis, etc.) prevailed in the administration. In order to achieve this they weakened Mavrokordatos and eliminated Negris and Ypsilantis. In addition, they were assisted by the expectant attitude of the notables of Hydra and Spetses. Their political authority was enhanced by the taxes from the Peloponnese which they controlled and which constituted until then the most important source of financial support for the Revolution.

Nonetheless, the internal controversy had not finished. In spring 1823 the suppression of the office of Commander-in-Chief held by Kolokotronis revealed that the organs of the administration were employed to enfeeble political rivals and strengthen political allies. This time Kolokotronis, who had been elevated to significant political heights, was the target. The tension was controlled until the autumn. However, in November 1823 the tension came to a head when Kolokotronis and Petrobeis Mavromichalis persecuted the 'politicians' from Nauplion and tried to form their own administration. The Peloponnesian notables fled to Kranidi, a coastal village opposite Hydra, and formed a new administration, joining forces with the notables of the islands. This second administration was controlled by the powerful economic and political agents of Hydra - Georgios and Lazaros Kountouriotis - but Alexandros Mavrokordatos and Ioannis Kolettis played a part as well. The former maintained contact with Lord Byron and the philhellenic Committee of London and became the receiver of the loan. With this money, Kolettis activated his relations with the chieftains of Rumeli, Epirus, Thessaly and other regions, which constituted the army of the so-called Administration of Kranidi. The civil conflict had already broken out.