He served as Prime Minister of the Cook Islands from 11 February 2002 until 11 December 2004, and later as High Commissioner to New Zealand.
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.
[8] A few months later in January 2003 he sacked Deputy Prime Minister Geoffrey Henry, replacing him with Democratic leader Terepai Maoate.
[13] Lyon was later banned from the Cook Islands,[14] and Woonton attempted to sue those critical of the decision to allow him in for defamation.
[16] When the Cook Islands Herald published a satirical letter questioning this change in policy, Woonton attempted to have them prosecuted for criminal libel.
While awaiting the result of electoral petitions, Woonton announced a new coalition with the Cook Islands Party.
[26] Shortly after being sacked he joined a Wellington-based development firm which planned to build a new private hospital on Rarotonga.