Ngoupandé fell into a dispute with President Patassé over the speed of these reforms, and resigned in favour of Michel Gbezera-Bria in early 1997.
Standing as his party's candidate in the presidential election of 19 September 1999 (won by the incumbent Patassé), he received 3.14 percent of the vote, in sixth place.
The election marked a return to democratic rule after the coup d'état of 15 March 2003, which installed Gen. François Bozizé as president of an interim government backed by Chad.
In his campaign, he emphasized the need to bring peace and stability to the country, especially those areas most affected by rebel activity before the coup.
[10] He served as Minister of Foreign Affairs until September 2, 2006, when he left that position in a cabinet reshuffle and instead became special advisor to Bozizé.