Once in National Assembly of Kenya, he was first appointed as an Assistant Minister for Agriculture before he was transferred to the Ministry of Education and later to the Ministry of Information and Tourism. During his five years in the National Assembly, Wamukoya is credited with playing a major role in drafting the sugar bill and championing the rights of sugarcane farmers. Wamukoya is also credited with working hard to have the important Mumias-Busia road tarmacked. This road is a major commercial highway in the western Kenya region. Believing that education should be available for all, he is also credited with launching an education bursary fund for the education of needy and bright children. He also oversaw the largest expansion in schools, both primary and secondary, in his constituency since independence. He also initiated several projects that have largely benefited the lives of Matungu residents. These include support of self-help groups, development of youth empowerment programs and enhancement of provision of medical facilities.
All this success was however not enough to save him from the National Rainbow Coalition (NARC) euphoria that swept the country in the 2002 elections. In 2002 he lost his seat to David Were who contested on a NARC ticket. Wamukoya is still active in the politics of Western Kenya and still a force to be reckoned with in Matungu. He left KANU for the Liberal Democratic Party in 2004 and has risen to the level of branch chairman for the Matungu branch. However due to the ever changing landscape of Kenyan politics, Wamukoya has constantly been shifting his party preference as the preferences of his constituents change. In 2005 he briefly joined Orange Democratic Movement (ODM-Kenya) which was then touted to give incumbent Mwai Kibaki a run for his money in the 2007 general election. This was not to last long though. In early 2007 Wamukoya appointed a special team to survey his constituents to find out what their preference was. Based on the results of their survey, which showed that majority of the electorate were pro-government, Wamukoya joined Narc-Kenya, then widely believed to be Mwai Kibaki's Party of choice for re-election. However Matungu politics is constantly evolving and following President Mwai Kibaki's announcement that he will seek re-election of a Party of National Unity (PNU) ticket, the electorate of Matungu has subsequently shifted its allegiance to this new entity. He is expected to contest the Matungu seat on a PNU ticket in the General Elections called for 27 December 2007.
Many analysts on the ground believe that he will regain the Matungu seat, although by a small margin. This is largely because the incumbent has failed to deliver on his 2002 promises and all projects initiated by Wamukoya have stalled ever since. There is huge discontent with the incumbents constant absence from the constituency and lack of time for the people.
The constituency is unique in that it is a cosmopolitan area. Apart from the dominant Wanga sub-clan, other smaller clans and people from communities like Bukusu and Luo reside in the area. Clannism could therefore feature in Matungu politics with the dominant Abashitsetse keen to reclaim the seat.
Mr Were is said to be of Luo origin whose parents migrated to the area long ago. Mr Murunga is also said to be from neighbouring Bukusu community in Bungoma. The two may find it difficult if opponents harp on the issue of their paternity. Wamukoya is riding high on this issue as he is likely to be the only candidate from the dominant clan to make it as far as the ballot box. This coupled with is adequate resources and vast knowledge of the constituency are thought to give him an extra edge over his opponents.
However, like in 2002, last minute euphoria for change could sweep the constituents to blindly vote for candidates standing on an ODM ticket.