Discontent with Kapodistrias' policy began to take the form of organized opposition, especially after the Fourth National Assembly (summer of 1829). In this National Assembly the suspension of the constitution, the dissolution of the Parliament and the concentration of all power in the hands of the Governor were confirmed. In other words, the marginalization of the political factions which had until then held sway in political life was ascertained. Despite the fact that Kapodistrias appeared to maintain a neutral and mistrustful attitude toward everyone, gradually he approached Kolokotronis and his faction, which was composed of relatives and people that the Governor trusted. This approach led gradually to the creation of a 'Kapodistrian' or 'governmental' political formation, as the split groups of the opposition rallied and coordinated their action. Moreover, although he tried at first to get rid of his reputation as a Russophile, his relation with Russia became stronger and stronger, while the ambassadors of Great Britain and France observed a neutral attitude or even one of opposition.

Hydra and Mani constituted the most important centres of opposition and from the beginning of 1830 the power of the Governor there was mostly superficial. Districts with a privileged economic and administrative regime during the Ottoman occupation and the Revolution were a source of tension and secession movements. Mani, the bulwark of the Mavromichalis family, was constantly in a turbulent situation from the spring of 1830. Many uprisings occurred, the most important of which was in the summer of 1831 when Kalamata was conquered. The movement was probably traditional in the sense that it aimed to maintain the special privileges of the region. Similar causes were to motivate the people of Mani in the first armed uprising of the kingship of Otto (1834). At Hydra, where the family of Kountouriotis prevailed, the notables from the Morea and the islands as well as Alexandros Mavrokordatos had assembled. Their opposition policy was directed, at least in the beginning, to the reversal of Kapodistrian policy by limitating the powers of the Governor and subjecting him to constitutional control. The occupation of the naval yard at Poros by Miaoulis and the blowing up of part of the Greek fleet in the summer of 1831 was an extreme expression of the 'constitutionalists'. Ioannis Kolettis, held responsible for the restricted military movement of Tsamis Karatasos in east-central Greece in the summer of 1830, went along with the constitutionalists. The assassination of Kapodistrias on 27 September 1831 at Nauplion by two members of the Mavromichalis family increased the tension and intensified the opposition. The two sides started a new round of armed conflict which was terminated on the eve of the arrival of Otto and the members of the regency in January 1833.