As an ally of Deputy Minister Mihkel Oviir, he was appointed Auditor General in the spring of 1998.

In the Riigikogu (Estonian parliament) elections in 2003, Parts surprisingly gained a majority among the right-of-centre parties, and as a result, he was charged to form a new government coalition and became Prime Minister of Estonia.

Vaher had established a quota system of how many civil servants had to be prosecuted every year (per county), which is seen as reminiscent of Stalinist purges by many Estonians, a measure that Parts had endorsed.

Parts' term as Prime Minister officially ended on 12 April 2005 when the Riigikogu confirmed his successor Andrus Ansip.

[5] After calling some members of the Lithuanian government "fools" in a 2014 interview with the Wall Street Journal about the joint Rail Baltic infrastructure project, Parts found himself under heavy fire in both countries.