In the aftermath of the failure of the Fiji coup of 2000, a coup which Nailatikau strongly opposed, he was nominated for the position of Prime Minister, to help rebuild Fiji's shattered institutions. He withdrew his nomination, however, in favour of Laisenia Qarase, who was considered more of a consensus candidate, but became Deputy Prime Minister and Minister for Fijian Affairs in the interim Cabinet. In 2001, after democracy had been restored in a general election, he defeated, by a vote of 41 to 29, Joeli Kalou for the position of Speaker of the House of Representatives, a position he held until after the 2006 elections.