In the parliamentary election of 2001, he contested the Macuata Fijian Communal Constituency for the United Fiji Party (SDL), but was defeated by Isireli Leweniqila of the Conservative Alliance (CAMV). On 23 February 2006, he announced his candidacy for the Presidency or Vice-Presidency. When Great Council of Chiefs met on 8 March, however, it reelected Ratu Josefa Iloilo as President and Ratu Joni Madraiwiwi as Vice-President. See Fiji presidential election, 2006.
Katonivere has taken some unusual positions for a Vanua Levu chief. He announced on 2 June 2005 that he was withdrawing his previous support for the controversial Reconciliation, Tolerance, and Unity Bill, after Attorney-General Qoriniasi Bale clarified that the legislation included provisions for amnesty to be granted to persons convicted of involvement in the Fiji coup of 2000. "I do not support its amnesty provisions," Katonivere said. "The majority of our sons who were convicted have accepted, suffered and served sentences for their deeds. People should learn to respect the law and abide by it, and face the consequences. Only then will they learn from their mistakes ... To suspend or hinder the process of law by the judiciary will not be championed by me."
Katonivere has a reputation as a strong conservationist and has taken a stand against the killing of turtles in his province. Katonivere is a self confessed "Conservation Convert"- this came about when he discovered that the Great Sea Reef, known locally as Cakau Levu is the third largest barrier reef in the world. He has also taken action against illegal fishing. As of 10 March 2006, his handling of one such incident is the subject of a police investigation. A Seaqaqa police officer told the Fiji Sun on 8 March that a complaint had been lodged by a Ratu Orisi Turogo, whose fishing boat and 300-kilogram catch had allegedly been confiscated at knife-point on Katonivere's orders. His F$7000 fishing net had also been destroyed, and the engine of his boat damaged, Turogo claimed. Katonivere allegedly demanded $F2000 for the return of his boat. Elipi Vocea, Police Commander of the Northern Division, supported Turogo's version of events, and said that what the villagers had done at Katonivere's behest was unlawful.
Katonivere's defenders maintain that the confiscation of the fishing gear was carried out by a licensed fish warden from Kia Island - which comes under Katonivere's traditional fishing grounds where the man was caught fishing. Under Fiji laws, the fish warden may confiscate fishing gear of suspected poachers who encroach on declared "no take" areas.