Yabaki was a strong critic of some policies and decisions of the Qarase government of 2000 to 2006, including the early release from prison of persons convicted on charges related to the Fiji coup of 2000, and opposed controversial legislation seeking to establish a Commission empowered to propose amnesty for such persons.
While most opponents of the Qarase government were, at the most, muted in their criticism of the military coup of 5 December 2006, Yabaki strongly opposed both the coup itself and the actions of the Military in the leadup to it. Before the coup took place, Fiji Village said on 28 November that he had written to Commodore Frank Bainimarama, Commander of the Republic of Fiji Military Forces, calling on him to tone down his rhetoric and enter into dialogue with the government. Yabaki reiterated his own opposition to the same government policies that the Military was opposing, but insisted that it was not the role of the Military to oppose an elected government.
Following the coup, Fiji Television revealed on 16 December that he had written to Bainimarama on 12 December, urging the Military to hand power back to the civilian President, Ratu Josefa Iloilo, and negotiate an amnesty for himself and his soldiers. He agreed that the Qarase government had been divisive and acknowledged that there were allegations of corruption, but said that neither posed such a credible threat to the state as to justify military intervention. On 23 December, the Fiji Sun quoted him as endorsing a proposal from the Great Council of Chiefs to establish an interim government of national unity.
The Methodist Church of Fiji and Rotuma dismissed Yabaki from the pulpit in 2001. No reason for the dismissal was given at the time, although political disagreements were widely thought to be involved. A claim endorsed by the Fiji Times, which asserted on 27 January 2006 that Yabaki's excommunication followed church opposition to his political activism in the wake of the 1987 coups. He continued to use the title Reverend.