[7] Teme remained in that office after the transition of East Timor to independence on 20 May 2002, as part of the I Constitutional Government led by Prime Minister Mari Alkatiri.

[9][10][11] Due to the unrest in East Timor in 2006, Prime Minister Alkatiri was forced to resign, and within Fretilin there was an attempt to remove him as its general secretary.

Teme joined the Fretilin Mudança reform movement, and in the 2007 presidential election campaign he supported the new prime minister and independent candidate José Ramos-Horta against his party leader Francisco Guterres.

[12] In August 2007, Teme became Secretary of State for the Region of Oecusse in the IV Constitutional Government under Prime Minister Xanana Gusmão, although his party, Fretilin, was in opposition to the ruling coalition.

As the FM failed to overcome the four percent threshold hurdle in the election, Teme lost his seat in the National Parliament.