Running for re election on a Party of National Unity ticket, defending his seat as Member of parliament for North Imenti Constituency, he was defeated by Silas Muriuki, who was running on a Mazingira Green Party of Kenya ticket.
Following allegations that he had been involved in the Anglo Leasing Scandal, he decided to resign as Finance Minister on 1 February 2006.
[2] Despite there being no investigation report clearing Mwiraria, President Mwai Kibaki appointed him Minister for Environment on 24 July 2007.
Mwiraria features prominently in audio recordings released on the internet in 2006 by John Githongo, exiled former Permanent Secretary in the Kenya Government, which indicate Mwiraria was trying to stop Githongo's inquiries into the theft of over 700 million US Dollars in a series of 18 security related contracts, colloquially called Anglo Leasing.
[3] In December 2007, Mwiraria, Nicholas Biwott, and Ramniklal Panacha Shah were banned from traveling to or through the United Kingdom due to the then pending corruption charges.