In February 2002 Woonton resigned his portfolios and tabled a motion of no confidence against Maoate. The motion failed, and Woonton returned to the government. Three days later, Maoate resigned after losing a second confidence vote, and Woonton became Prime Minister. Woonton's premiership was beset by chaos and allegations of corruption. In May 2002, shortly after taking office, he was cleared of bribery allegations over claims he had approved the use of public money to fly an independent MP and his wife to New Zealand so she could receive medical treatment. In September 2002 he threatened to deport the publisher of the Cook Islands Independent after it published a story alleging he had used public money to purchase furniture for his private residence. In November 2002 he sacked Justice Minister Norman George, formed a new coalition with both the Democratic Party and Cook Islands Party, and promised early elections. A few months later in January 2003 he sacked Deputy Prime Minister Geoffrey Henry, replacing him with Democratic leader Terepai Maoate. In November 2003 Maoate in turn resigned after he tabled a motion of no confidence in the government. Later that month Woonton was officially elected leader of the Democratic Party, replacing Maoate. He was replaced again by Maoate in May 2004. In December 2003 Woonton's government faced allegations that it was selling residency, after it granted residency to convicted New Zealand businessman Mark Lyon in exchange for a $150,000 bond. Lyon was later banned from the Cook Islands, and Woonton attempted to sue those critical of the decision to allow him in for defamation. In May 2004 he made a state visit to China, in which he accepted US$2.5 million in aid in exchange for recognising that Taiwan was part of China. When the Cook Islands Herald published a satirical letter questioning this change in policy, Woonton attempted to have them prosecuted for criminal libel. Shortly afterward he dissolved Parliament for the election. At the 2004 election Woonton's government retained its majority, but Woonton was nearly defeated. While awaiting the result of electoral petitions, Woonton announced a new coalition with the Cook Islands Party. He was subsequently expelled from the Democratic Party and formed his own party, the Demo Party Tumu. On 12 December 2004 a recount found that the result in Woonton's electorate of Manihiki was a tie. Woonton resigned as Prime Minister, and was replaced by Jim Marurai. He did not contest the resulting 2005 Manihiki by-election. Following the election, the Cook Islands Court of Appeal ruled that Woonton's Cabinet had bribed voters in the electorate of Titikaveka in an effort to secure the election of Cabinet Minister Robert Wigmore.
Post-political career
In early 2005 Woonton was appointed High Commissioner to New Zealand, replacing Tom Davis. He was sacked in March 2006, following accusations that he was plotting with members of parliament to end Marurai's government. Shortly after being sacked he joined a Wellington-based development firm which planned to build a new private hospital on Rarotonga. He now works as a doctor in Auckland. In 2011 he was appointed to the Auckland Council's inaugural Pacific People’s Advisory Panel.
